% LuaLaTeX or XeLaTeX
\documentclass[12pt,twoside,a4paper]{book}
\usepackage[innermargin=15mm,outermargin=25mm]{geometry} % Set geometry
% Since you set the second page to "1", the margins will be mixed up by TeX!
% To see the effect I've set different margins.

% Set languages and fonts
\usepackage{polyglossia,xunicode} % Multilanguage support
\usepackage{fontspec} % Include fonts configuration
\usepackage[%
  libertine={Ligatures=TeX,Numbers=OldStyle},% use TeX ligatures and oldstyle numbers
  biolinum={Ligatures=TeX,Numbers=OldStyle},%
  mono={Scale=0.85},%
]{libertineotf}

\setmainlanguage{latin}
\setotherlanguage[babelshorthands=true,spelling=old]{german} % just for the example
% You will probably use this:
%\setotherlanguage{russian}
\setotherlanguage[variant=polytonic]{greek}

% Other packages, as far as possible in alphabetical order
\usepackage{etoolbox} % Provides a lot of helpful commands and tools,
                      % needed here for "\ifblank"

\usepackage{fancyhdr} % Include beautiful headers
% Set headers, footers and footnotes
  \fancyhead{}
  \fancyfoot{}
  \pagestyle{fancy}
  \renewcommand{\headrulewidth}{0pt}
  \renewcommand{\cleardoublepage}{\clearpage}
%  \fancyfoot[LE,RO]{\thepage} % Looks after page count; since you set the second page
                              % to "1", the numbers will be set to the inner margin!
  \fancyfoot[LO,RE]{\thepage} % for setting the page number to the outer margin here

\usepackage{indentfirst} % Indent first paragraph after section header, too

\usepackage{ledmac} % For setting critical editions
  \lineation{page} % page-wise line counting
  \linenummargin{outer} % line numbers on outer margin of twoside document,
                        % looks after page count; since you set the second page
                        % to "1", the numbers will be set to the inner margin!
  \sidenotemargin{inner} % for side notes, e.g. caput & sect;
                         % should be the opposite of "\linenummargin"!
  \renewcommand{\notenumfont}{\normalfont\bfseries}
% "ledmac" provides by default 5 levels of apparatus, "\Afootnote" ... "\Efootnote"
%  \let\variant\Afootnote % copy meaning of command "\Afootnote" into the new
                         % "\variant", that is the first level of apparatus
% better solution:
  \newcommand{\variant}[3][]{\edtext{#2}{\ifblank{#1}{}{\lemma{#1}}\Afootnote{#3}}}
%  \let\comment\Bfootnote
% better solution:
% you probably want to use here "\textrussian"
  \newcommand{\comment}[3][]{\edtext{#2}{\textgerman{\ifblank{#1}{}{\lemma{#1}}\Bfootnote{#3}}}}
  % comments set only for the first text-section
%
  \footparagraph{A} % apparatus, level A, as one single paragraph (here "\variant")
%
% Redefining the appearance of one apparatus level is difficult:
  \makeatletter % switches the meaning (exactly the catcode) of the "@" sign,
                % because we have to use some "@"-containing commands
  \renewcommand*{\twocolfootfmt}[3]{% switch to set comments in two columns below
    \normal@pars
    \hsize .45\hsize
    \parindent=0pt
    \tolerance=5000
%    \raggedright
    \RaggedRight % from package "ragged2e"
    \leavevmode
    \strut{\notenumfont\printlines#1|}\enspace
%    {\select@lemmafont#1|#2}\rbracket\enskip
    {\select@lemmafont#1|\textsf{\slshape#2}}\thinspace:\enskip
    #3\strut\par\allowbreak}
  \makeatother % switches back to the default catcode in LaTeX code outside of
               % document classes or packages
  \foottwocol{B} %  apparatus, level B, as one single paragraph in two columns (here "\comment")
%
% You can use ordinary footnotes, but "ledmac" provides by default 5 additional footnote series,
% the counter for the first of them is redefined here, just to show you the effect
\renewcommand*{\thefootnoteA}{\alph{footnoteA}}

% Create further commands
\newcounter{Caput}\newcounter{Sect}
\newcommand*{\caput}{\stepcounter{Caput}\stepcounter{Sect}%
                     \ledsidenote{\Roman{Caput}.\arabic{Sect}}}% "\ledsidenote" from "ledmac"
                    % "\ledsidenote" will be set according to "\sidenotemargin"
% In "Pro Murena" the sections are continuously counted upwards,
% otherwise we would have to do this:
% \newcounter{Caput}\newcounter{Sect}[Caput]
% \newcommand*{\caput}{\refstepcounter{Caput}\stepcounter{Sect}%
%                      \ledsidenote{\Roman{Caput}.\arabic{Sect}}}
\newcommand*{\sect}{\stepcounter{Sect}\ledsidenote{\arabic{Sect}}}

\newcommand*{\Yat}{Ѣ}
\newcommand*{\yat}{ѣ}
\newcommand*{\Ou}{Ȣ}
\newcommand*{\ou}{ȣ}
\renewcommand*{\ss}{ſſ}
\newcommand*{\s}{ſ}

% Main document
\begin{document}

% Create title page
\title{Marci Tulli Ciceronis\\ Pro Lucio Licinio Murena oratio}
\author{Дмитрий Сергеевич Селютин}
\date{} %%% Suppresses the printout of the date (but adds a bit vertical space)

\maketitle

% Create document
\setcounter{page}{1}% It's better to refrain from this!
\selectlanguage{latin}

\section*{Pro L.~Licinio Murena\footnoteA{\textgerman{\mdseries Source
                                for German commentary:
                                \texttt{http://books.google.de/books?id=vklQAAAAcAAJ}.}}}


\begingroup % For long text parts this is better to read than the
            % short form "{"; grouping needed for "\autopar"
\beginnumbering % ledmac
\autopar % ledmac
% "\autopar" will break, if you put footnotes (and surely other stuff, too)
% inside extra groups, as you did it

\caput\comment[quae precatus {\dots} sum]{\variant[quae precatus]{Quae
precatus}{\emph{Naugerius}~: quae deprecatus \emph{codd.} (\emph{cf. Quintil.}
ix. 4. 107, \emph{Creticus et initiis optimus}. Quod precatus a dis immortalibus
sum)~: quod precatus \emph{Halm} (2) \emph{cum Quintil.}} \variant{a}{ς1χψ~: ab
ς2BAπ} dis immortalibus sum}{Der präsidierende Magistrat eröffnete die Comitien
mit einem Opfer und Gebet, \emph{precatio}, s. Liv.~39,~15,~1:
\textlatin{\emph{consules in rostra escenderunt, et contione advocata cum
sollemne carmen precationis, quod praefari solent priusquam populum adloquantur
magistratus, peregisset consul, ita coepit}}.}, iudices, more institutoque
maiorum illo die quo \comment{auspicato}{s. Madvigs lat. Sprachl. \S~429.}
comitiis centuriatis L.~Murenam consulem \comment{renuntiavi}{Nachdem der Praeco
das Resultat der Abstimmung der einzelnen Centurien verkündet hatte, erfolgte
die feierliche Renuntiation des Gewählten durch den Magistratus, der die
Wahlhandlung geleitet hatte.}, ut ea res \comment{mihi
\variant{fidei}{\emph{Lambinus}~: fides ςAπ, \emph{om.} Bχψ}
magistratuique}{eine alte Formel, wie Ennii fragm. Ann.~111 (ed. Vahl) zeigt:
\textlatin{\emph{Quod mihi meaeque fide \emph{(=~fidei)} et regno vobisque
Quiritis [\dots]}}, und die bei Varro de ling. lat.~VI, \S~86 erhaltene Formel
von den Censoren: \textlatin{\emph{Quod bonum fortunatum felixque salutareque
siet populo Romano Quiritium {\dots} mihique collegaeque fidei magistratuique
meo [\dots]}}. In dieser Formel scheint \emph{fides} im Sinne von
`Gewissenhaftigkeit, Pflichttreue, redliches Wollen' zu stehen.} meo,
\comment{populo plebique}{Mit dieser Verbindung, die nur in Gebeten,
Orakelsprüchen und anderen alten Formeln vorkommt, wird das aus Patriciern und
Plebejern bestehende röm. Gesammtvolk bezeichnet; sie stammt aus einer Zeit, wo
die Patricier allein Vollbürger waren und als solche den \emph{populus}
ausmachten.} Romanae bene atque feliciter eveniret, \variant{eadem}{idem
\emph{Boot}} precor ab isdem dis immortalibus \comment[ob {\dots} obtinendum]{ob
eiusdem hominis consulatum una cum \comment{salute}{`Freisprechung', durch die
sein bürgerliches Wohl bedingt ist.} obtinendum}{`jetzt wo es sich darum handelt
dass' etc.}, \comment{et ut}{schließt sich an \emph{idem} an~=
\textlatin{\emph{precor ut ea res feliciter eveniat et ut}} etc.} vestrae mentes
atque sententiae cum populi Romani voluntatibus suffragiisque consentiant, eaque
res vobis populoque Romano pacem, tranquillitatem, otium concordiamque adferat.
Quod si illa sollemnis comitiorum precatio consularibus auspiciis consecrata
tantam habet in se vim et religionem quantam rei publicae dignitas postulat,
idem ego sum precatus ut eis quoque hominibus quibus hic consulatus me rogante
datus esset ea res fauste feliciter prospereque eveniret.

\sect Quae cum ita sint, iudices, et cum omnis deorum immortalium potestas aut
\variant{translata}{tralata σπ} sit ad vos aut certe communicata vobiscum, idem
\variant{consulem}{\emph{Boot}~: consul ei (eum ω) \emph{codd.}} vestrae fidei
commendat qui antea dis immortalibus commendavit, ut eiusdem hominis voce et
declaratus consul et defensus beneficium populi Romani cum vestra atque omnium
civium salute tueatur. Et quoniam in hoc officio studium meae defensionis ab
accusatoribus atque etiam ipsa susceptio causae reprensa est, ante quam pro
L.~Murena dicere instituo, pro me ipso pauca dicam, non quo mihi potior hoc
\variant{quidem}{\emph{Lag.} 9~: quidem in \emph{cett.}} tempore sit offici mei
quam huiusce salutis defensio, sed ut meo facto vobis probato maiore auctoritate
ab huius honore fama fortunisque omnibus inimicorum impetus propulsare possim.

\caput Et primum M.~Catoni vitam ad certam rationis normam
\variant{derigenti}{ςAπφ~: dirigenti χψω} et diligentissime perpendenti momenta
officiorum omnium de officio meo respondebo. Negat fuisse rectum Cato me et
consulem et legis ambitus latorem et tam severe gesto consulatu causam
L.~Murenae attingere. Cuius reprehensio me vehementer movet, non solum ut vobis,
iudices, quibus maxime debeo, verum etiam ut ipsi Catoni, gravissimo atque
integerrimo viro, rationem facti mei probem. A quo tandem, M.~Cato, est aequius
consulem defendi quam a consule? Quis mihi in re publica potest aut debet esse
coniunctior quam is cui res publica \variant{a me iam}{\emph{Klotz}~: ame/77/a ς
(\emph{m.} 2 \emph{in lac.})~: a me una \emph{cett.}~: a me uno
\emph{Lambinus}~: a me in manum \emph{Müller}~: \emph{fort.} a me universa
(universa a me \emph{Landgraf})} traditur sustinenda magnis meis laboribus et
periculis sustentata? Quod si in \variant{eis}{iis (is) φ1~: his \emph{cett.}}
rebus repetendis quae mancipi sunt is periculum \variant{iudici}{\emph{om.} A}
praestare debet qui se nexu obligavit, profecto etiam rectius in iudicio
consulis designatiis potissimum \variant{consul}{\emph{del. Madvig}} qui
consulem declaravit auctor benefici populi Romani defensorque periculi esse
debebit.

\sect Ac si, ut non nullis in civitatibus fieri solet, patronus huic causae
publice constitueretur, is \variant{potissimum summo}{\emph{Madvig}~: potissimo
(-e ψ2) \emph{codd.}} honore adfecto defensor daretur qui eodem honore praeditus
non minus adferret ad dicendum auctoritatis quam facultatis. Quod si \variant{e
portu}{\emph{Quintil.} v. 11. 23~: portu \emph{B}ψ~: portus \emph{cett.}}
solventibus \variant{ei qui}{qui \emph{Quintil.}} iam in portum ex alto
invehuntur praecipere summo studio \variant{solent et}{ψ2~: solent ei ςAπφω~:
solent eis χψ1} tempestatum rationem et praedonum et locorum, quod natura
\variant{adfert}{fert \emph{Victorius (contra Quintil.)}} ut eis faveamus qui
eadem pericula quibus nos perfuncti sumus \variant{ingrediantur}{πφω,
\emph{Quintil.}~: ingrediuntur ςAχψ}, quo tandem me \variant{esse animo}{animo
esse \emph{Quintil.}} oportet prope iam ex magna iactatione terram videntem in
hunc cui video maximas \variant[rei p.]{rei publicae}{\emph{om. Quintil.}}
tempestates esse subeundas? Qua re si est boni consulis non solum videre quid
agatur verum etiam providere quid futurum sit, ostendam alio loco quantum
salutis communis intersit duos consules in re publica Kalendis Ianuariis esse.
\endnumbering % ledmac
\endgroup % for long text parts this is better to read than the
          % short form "}"; grouping needed for "\autopar"
\end{document}