To test your configuration you can do the following.
For tuning purpose i'm using a Windows machine and download build (0.81.090) here http://www.kaashoek.com/files/
I then backup existing comskip.ini and put my test/tuning comskip.ini that looks like this:
(more info here http://www.kaashoek.com/files/tuning.htm)

verbose=10				; show a lot of extra info, level 5 is also OK, set to 0 to disable
detect_method=47		; For testing purpose this should be set to 47, 1=black frame, 2=logo, 4=scene change, 8=fuzzy logic, 16=closed captions, 32=aspect ration, 64=silence, 128=cutscenes, 255=all
delete_logo_file=0		; set to 1 if you want comskip to tidy up after finishing
output_framearray=1		; Only for tuning (set to 1) Create a big excel file for detailed analysis, set to 0 to disable
output_data=1			; Only for tuning (set to 1) Create a dump of the user data channel, used for CC and XDS (such as V-Chip info). Can be use together with output_framearray to remote debug CC decoding
output_debugwindow=1	; Only for tuning (set to 1)
non_uniformity=1000		; Only for tuning (1000 default 500)
max_volume=1000			; Only for tuning (1000 default 500)
output_edl=1
edl_skip_field=3        ; 0 - Cut, 1 - Mute, 2 - Scene Marker (if start and end times are specified, the end time is used), 3 - Commercial Break

You should use edl_skip_fields=3.
Explanation for edl setting http://kodi.wiki/view/Edit_decision_list

Run a sample recording (with commercial and show pieces) and wait until it's finished.

When it's finished you quickly can check how it performed by dropping (and releasing the txt file over comskipGUI.exe
This will load your commercial brakes. You can navigate with arrow keys or pgup/pgdn buttons (hit F1 for full key list)
This way you can validate if it's correct.

If something is not right, change your comskip.ini configuration using instructions found in previous link and drop your csv file over comskipGUI.exe again to generate new txt/edl file (no need to run full process again)
And validate again.

The comskip tuning guide also says to check certain values from generate csv but i never needed to do that.
(Needed for min and max sound, black levels etc.)

After some testing and help from Erik (comskip dev) my ini file looks like this (it's this small because all default values will be used if not defined)

verbose=0				; show a lot of extra info, level 5 is also OK, set to 0 to disable
detect_method=111		; 1=black frame, 2=logo, 4=scene change, 8=fuzzy logic, 16=closed captions, 32=aspect ration, 64=silence, 128=cutscenes, 255=all
delete_logo_file=0		; set to 1 if you want comskip to tidy up after finishing
output_framearray=0		; Only for tuning (set to 1) Create a big excel file for detailed analysis, set to 0 to disable
output_data=0			; Only for tuning (set to 1) Create a dump of the user data channel, used for CC and XDS (such as V-Chip info). Can be use together with output_framearray to remote debug CC decoding
output_debugwindow=0	; Only for tuning (set to 1)
non_uniformity=500		; Only for tuning (1000 default 500)
max_volume=500			; Only for tuning (1000 default 500)
output_edl=1
edl_skip_field=3        ; 0 - Cut, 1 - Mute, 2 - Scene Marker (if start and end times are specified, the end time is used), 3 - Commercial Break

As you can see it isn't that different then the default one. If you look close you will see only 1 value being modified and that is the detect_method to 111, this works perfect in my case.

Once you have debugged your file and configuration but still have wrong commercial cuts you could ask for help here: http://www.kaashoek.com/comskip/viewtopic.php?f=5&t=34

Some extra info can be found in SynoCommunity wiki https://github.com/SynoCommunity/spksrc/wiki/Comskip

My current PP script is:
(using this so i can re-use logo files grabbed earlier to speed up proces)
#!/bin/sh

# Variables
INPUTVIDEO=$1
CHANNEL=$2

TVHEADENDPP="/volume1/@appstore/tvheadend-testing/var/"

echo "*****" > ${TVHEADENDPP}/tvheadendpp$$.log
echo "***** INPUT FILE = $INPUTVIDEO *****" >> ${TVHEADENDPP}/tvheadendpp$$.log
echo "***** CHANNEL NAME = $CHANNEL *****" >> ${TVHEADENDPP}/tvheadendpp$$.log
echo "*****" >> ${TVHEADENDPP}/tvheadendpp$$.log

COMSKIPPATH="/volume1/@appstore/comskip/bin/comskip"
COMSKIPINI="/volume1/@appstore/comskip/var/comskip.ini"
COMSKIPINI_DEL_LOGO="/volume1/@appstore/comskip/var/comskip-del-logo.ini" #same ini only value delete_logo_file changed to 1, delete_logo_file=1

if [ "$CHANNEL" == "RTL 4 HD" ]; then
  $COMSKIPPATH --ini=$COMSKIPINI_DEL_LOGO --logo=/volume1/@appstore/tvheadend-testing/var/RTL-4-HD.logo.txt $INPUTVIDEO 2>&1 </dev/null
else
  $COMSKIPPATH --ini=$COMSKIPINI $INPUTVIDEO 2>&1 </dev/null
fi[/code]

TVHeadend post-processor command used is: /volume1/@appstore/tvheadend-testing/var/tvheadend-pp.sh "%f" "%c"