As a rule of thumb we recommend that ANY transaction affecting orders, shipping, receiving, production or inventory quantities should originate from All Orders for the following reasons:
All Orders captures location information
All Orders captures lot and serial # information
All Orders provides more visibility into open orders and available inventory.
Sales Orders and Purchase Orders DO NOT get recorded in QuickBooks rather they are processed within All Orders as ship docs and receivers respectively. Ship Doc and Receiver are then recorded in QuickBooks as Invoices and Receiver respective using the Trigger or Button as described in What information is shared with QuickBooks or by having these transaction post in QuickBooks automatically in a batch (See Synchronization Options).
Generally activities involving cash (cash receipts, bill payments), payroll, or general ledger should be done within QuickBooks.
Some companies just want to use All Orders for production or generate purchase orders but continue to use QuickBooks for sales orders, shipping etc. This is completely acceptable however if desired you will need to update the quantities in All Orders to reflect the inventory quantities QuickBooks. To accomplish this task click Company --> Synchronize QuickBooks --> Reconcile With QuickBooks --> Reconcile to QuickBooks. See Resolving quantity difference between QuickBooks and All Orders.