Let's say you've got a check recorded in QuickBooks Online, but you also want to record the payment in Goodshuffle Pro.
You'll still record it in Goodshuffle (to avoid the project showing as 'Due'), but to avoid a duplicate payment entry in QuickBooks, just make sure to click 'Disable Sync' when recording the payment.
PS- Ideally you should record the offline payment in Goodshuffle Pro and sync it over to QuickBooks Online. That will save you from recording it twice. Recording in GSP and allowing it to sync over to QBO would save you some time.