Am I free to place the ad anywhere on my site? i.e. the footer If not, Can I place the ad on one page, but link back to another? Can I have 2 sites on one accoun?
As long as it's visible i think anything's fine. The ads have to be site-wide but you can link to anywhere you like (The ad has to get approved first). Shawn made some changes so that accounts can now be combined. I haven't really looked at it yet but I think that it means you can have more than one site per account.
You would signup for a 2nd account (for the different site), but you can bind it to your primary account.