[Setup]
AppName=My Program
AppVersion=1.5
DefaultDirName={pf}\My Program

[Run]
Filename: "{app}\MyProg.exe"; Parameters: "{code:GetVariableByIndex|1}"
Filename: "{app}\MyProg.exe"; Parameters: "{code:GetVariableByIndex|2}"

[Code]
var
  FirstVariable: string;
  SecondVariable: string;

function GetVariableByIndex(Param: string): string;
begin
  case Param[1] of
    '1': Result := FirstVariable;
    '2': Result := SecondVariable;
  end;
end;

procedure InitializeWizard;
begin
  FirstVariable := 'FirstVariable';
  SecondVariable := 'SecondVariable';
end;