I think a lot of Amazon affiliates have ebay listings on their website and vice-versa but you can't really combine them into one store if that's what you mean, because where would the shopper pay? During payment they will always have to be sent to one or the other checkout page.
I plan to have some content pages with ebay listings at the bottom and links to specific Amazon items in the text or on the sidebar. If someone is interested in left handed monkey wrenches they might buy one on Ebay and/or buy a book about them. Anything to improve the odds of a click.