So looking at the two stat pages you linked above, it seemed like #312 was performing better before I switched the layout around on March 17th. So maybe I should be switching things back?
I don't know. What is your criteria of better performance? If you are talking about profits, then, as I said, profits are not much affected by amount of ads embedded on your page, because there is no enough advertisers that pay per sale and AA just rewards you for unique impressions...
If your page contains 2 ad units, impressions of ad unit that loads first can be counted as unique, but impressions of other ad units on that page wont' be unique in terms of AA. Unique impression is a globally unique IP during 24hour period. It is done this way to limit the incentive for non-diligent publishers without banning them.
I hope more advertisers pay per sale in future, and then amount of unique impressions will become irrelevant, and you'll be able to measure performance by comparing earnings from goals (currently they are 0 for both of your ad units).
We welcome advertisers that want to integrate with our
Goal Tracking API to reward publishers per sale: we can offer free integration and advertising discounts. This all is not well documented, but we are working on that.