In a new post, Joe very clearly explains the difference between agency pricing and wholesale pricing.
Just remember one thing as you read his great post and all the comments:
If you sell a product to a bookstore for a wholesale price, you get the amount you charge the store. So if you are selling your book to a bookstore for a 50% discount, you get the 50%. It makes NO DIFFERENCE what the store sells it for.
Agency pricing is a system in which the publisher forces the store to sell the book only at a certain price. Period.
I agree with Joe on this one completely. Good post. Read the comments as well.