Yeah, you can have different google ad codes for each style I believe. I think instead of using the ad manager you can edit the ad template per theme and just slot in the google ad accordingly to each thread.
Not using the supercharged mod, as I don't really believe in mods that can speed up forums since I trust VB4. (Probably wrong but who knows)
Anyways, I wouldn't use that mod until the author fixes the problem. Your forum doesn't need it anyways since it's brand new and not calling as many database queries as a larger forum would. Looks like a powerful mod though with all the fix logs. Grats to the author.
Lately, I was planning on releasing a theme, but I've been custom working my CMS all day to get it too look different than the average cms:
http://buypoe.com (its a gamer site)
One problem I'm having with ads is every time I add an ad to the top right, below my toplinks, it pushes my header down and opens a huge gap of space.