To be honest I didn't see the ad on top of your homepage. But the position is ok. Not too obvious but not completely invisible either.
The two medium rectangles that you have in the middle of your content pages is a bit too much. You might need to commit to just one. Possibly the one on the left. I thought the image ad right in the middle of your content was too much.
But that's just my pennies worth. Really, what you need to do is let your visitors decide and that can take months of gradual experimentation.
Good luck with finding the right layout.