When the order becomes and invoice you should pay it. You may do it from Main menu > Database
Sales invoices
Unpaid invoices-orders
On the following screen you may search for the invoice o just select the invoice to pay
You will see that the invoice to pay should be higlighted. Make sure it is the right amount to pay and the date of payment the touch Continue
The next window you may touch the tag Pay or Complete payment
You may have a PDF with the send icon then touch Done
Keep in mind that orders should have an invoice number so you may pay them and be on sales reports