Do you need sync inventory with Amazon and QuickBooks?
For Amazon, we recommend using our Amazon summary. You will receive all fees and the order will match the Amazon deposit exactly. The downside is you must wait for the report, which is usually two weeks. Your inventory in QuickBooks will incorrect, until that report reaches QuickBooks.
If you need a live inventory sync, then you must sync individual orders with Amazon directly. With individual sales, you must match them to an Amazon deposit. ShipStation sends no Amazon fees, but our Amazon integration will send them for shipped orders. This means you must find the orders in your match deposits window, select them all, and add the fees in the deposits area.
Do you sell on multiple channels?
If you need no inventory sync with Amazon and you desire individual sales, you can use the ShipStation integration. As you add selling channels to ShipStation, there is no need to set-up more connections with Connex.
If you can wait two weeks for orders to reach QuickBooks and you want deposit matching made simple, then use the Amazon integration.