We have used QB for close to 5 years, looked at X-Cart, VP-ASP and more recently Business catalyst; in fact used them all, and they all had QB integration options.
Actually, now I look back on it, I moved from X-Cart because they couldn't really integrate, I gave up VP-ASP on the same, SalesForce was useless.. and now with IS at least I (and our book keeper) are happy. We put all sale transactions through The IS cart, and output a weekly product sales report which we post into QB.

After all, there's more date in IS than QB for customer lookup, so why bother trying to get every transaction across into QB?

BTW this grand revelation came about after much frustration attempting to use QB as sales reporting system (eccchh!) and taking a good long look at what we wanted from QB after that function was relocated to IS. Really, all we use QB for in general ledger accounts, balance sheet and P&L.