Hey, I'm sure you might get a better response. But I've been doing some research on this myself. Here are a couple guides. One uses dvrmstoolbox and the other uses comskip.
http://www.noelestep.net/blog/?p=43 Guide: Automated Ad Removal (DVRMS Toolbox)
It doesn't look like either integrate commercial skipping and only cutting of commercials. This makes me a little nervous because my experience with mythtv is that commercial flagging isn't flawless and will possibly cut stuff out that you don't want removed. Anyway, it sounds like commercial skipping will be included in the new tv engine. So, I'm just going to wait until it is out of beta.
Hope that helps.