I have all my ads on my forums, none on my main pages. (mainly because I havent taken the time to figure out how to do it). I am running two ads now, and one of them point to my sites home page, where the ads are not running. Does that penalize me in any way?
No. Stupid question indeed since it has been answered lots of times; it's OK to point ads to non-participating sites as long as they comply with the guidelines.