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in answer to your question.
Adwords (ads on the right), Premium Listings (ads at the top)
work compltely different from the standard search results on the main body of the page.
They will neither help your standard listings, nor will they harm them in any way.
Hope that helps.
basically Bid Management tools are provided by certain companies, who have been approved by Google, Overture etc, and they can control your bids (higher,lower) etc etc
You may want to spend an hour reading the The PPC Forum [webmasterworld.com]
This will give you valuable knowledge on the PPC market.
I admittedly never click the Adwords banners. I always just use the regular Google results I get and pick from that list. No..I don't know why, something psychological I guess...
I am an adwords advertiser and I NEVER click on the AdWords ads - but for a very different reason.
If I do find an ad interesting, I actually take the trouble of opening a new browser window and enter the URL in the browser (so that the advertisers do not lose money)
Call me crazy :)