I have set up several online businesses to work directly with Quickbooks. It works well as far as order processing and inventory management however there are some limitations. If you have more then 5000 products or if you receive more then 100 orders a day I would suggest a more robust accounting system. Quickbooks pro & enterprise work real well if your under those thresholds.

I have a several cleints running an online store both wholesale and retail as well as point of sale all integrated into a single company in Quickbooks.

Brian