Yes, the payment order will be issued for the remaining amount.
Example: I have a received invoice with a total amount of CZK 2,000. I have already paid CZK 1,000 in cash and need to create a payment order to the supplier for the remaining CZK 1,000.
-> Purchases -> Received Invoices (enter the received invoice) -> Services -> Cash Payment (in the table, select only the amount already paid — CZK 1,000) -> in the received invoice, use the "Add-on" button to change the payment method from "Cash" to "Bank Transfer" -> Services – Sign for Payment (if payment signing is enabled in your settings)
-> Money -> Payment Order -> New (select the bank account from which the invoice should be paid) -> Select Documents for Payment (select the document you want to pay — the outstanding amount will be pre-filled automatically) -> Send Payment Order
Be careful not to submit the same invoice to a payment order more than once! This means that until the document is settled by the bank, it can be added to a payment order an unlimited number of times.