Yes, the placement of the PPC ads has a significant effect on how often they get clicked.
The number of PPC ads displayed also has an effect. If a site contains too many PPC ads, it will appear to be spammy and visitors will leave rather than clicking on the ads.
If you are running AdSense ads on your site, Google has a great deal of guidance on proper placement in order to maximize clicks. Check their AdSense help section for more information.
Logan's advice is also excellent. "Test, test, test." What works on one site may not work on another. The only way to know for sure what works best on your site is to try things out and see.
(If you were hoping we would give you some magical "sure-fire technique" that promises to help you start earning thousands overnight with AdSense, you're bound to be disappointed. We don't make promises we can't keep.)