yeah, it's an older thread, but just now getting some of the ones read from when I was out of town
One I'm looking at right nwo for managing multiple stores is Atandra's T-Hub. Supposedly you can download sales from amazon seller central acct and then use that data to adjust inventory in quickbooks and then send that adjustment up to website. And, can do it the other way around as well - download sales from website to quickbooks and then push that out to amazon seller central.
So far I've used the download from website to quickbooks part, and that has worked well (well, once I got past some hurdles including figuring out why it wouldnt connect to quickbooks in vista - tech support couldnt find it, but I did). Havent tried the amazon aspect of it yet.
the full version that allows you to upload inventory to website is a bit pricey at $700, but...
other features include sending batch of sales to dazzle with a few clicks and printing packing slips with a few clicks. With T-Hub I can print packing slips and postage labels for a dozen packages in less than a minute.
It's not a perfect solution, because you still could end up selling the item twice since it depends on you pulling the info from one and updating to the other, but it's better than no solution.