Hi hilltop_account,

Currently, linking an invoice to the sales order is unavailable in QuickBooks Desktop. You'll want to create an estimate to track backorders and to convert it to invoice for the actual transaction.

To create an estimate

1. Click Customers on the upper menu.
2. Select Create Estimates.
3. Fill in the information such as the Customer Job, Item, Quantity and Total Amount.
4. Click Save & Close.

To convert it to invoice.

1. Open the estimate. 
2. Click Create Invoice on the upper part beside Attach File. 
3. Select if you want to create the entire estimate or only percentage.
4. Click OK,

Also, you can add and match bank feed in QuickBooks: Add and Match Bank Feed Transactions in QuickBooks Desktop.

Please let me know if you have any other concerns.I'll always right here to help.