Here you can ask your questions on how to use Comskip for the detection of commercials. Also questions on how to remove commercials are welcome
FWIW a little update here. I have turned off Plex's advertisement remover and have moved to MCEBuddy. Plex's commercial remover -- for whatever reason -- seems to leave commercials in place that seem to get detected with a second run of comskip. Very annoying. MCEBuddy appears to run two passes of ComSkip automatically. Additionally, it allows you to easily archive/backup source files and other nifty features.