Pretty clean and slick script, even up to the automated header image. What script is that? -- Yahoo Answers scraping it looks like.
From my experience, when you have clear "borders" to your ads, users are more likely to tune it out. The best way to learn is just to experiment. Although your current placement isn't bad, if your Amazon aff isn't converting anything, try replacing it with another ad block and place it between the Question and the Answer.
Unless you have a side navigation bar, you may get more clicks using that skyscraper block more intertwined with your content. Another good practice for me has been to randomize at least one block by script.
I have very limited experience (I'm rather new) but I also have moderate success and practice moving ads around. I think the best advice you can get is to simply experiment. moving around ads is easy. Change ad placement every week or two and look at your clicks. do they increase? do they decrease?