On the Sales Order, sales lines should be created as normal.

 A Payment Provider Account will be pulled through from the Customer Card with the Payment Method Code if one has been set.  The Payment Gateway Amount field will be empty initially but will be completed after payment has been taken, showing the amount received through the Payment Gateway.

Note - Sales documents with prepayment discount can result mismatch in issued payment and actual payment.  Payment terms can offer discounts if paid within a window of invoicing, however this has the potential of causing issues on unposted documents with payments being taken without any discount (which can change up until the invoice is posted).  Therefore, we do not support payment discount on sales documents alongside using Payment Gateway.