you need to setup comskip to detect commercials and comclean remove to them.
Search the forums and wiki for more info (I am not suitably well informed to give the best guidance on how to configure these progams).
It can be quite a lot of work to get comskip detecting commercials accurately across all your channels. Some people have to use a seperate config (comskip.ini) for each channel.
good luck
âIf this is the way Queen Victoria treats her prisoners, she doesn't deserve to have any.â