Invoices and sales
Record a payment on an invoice
Mark invoices paid (fully or in part), or let the bank deposit do it for you.
On an invoice, press Record payment, enter the amount, date and the account it went into. Part payments are fine; the invoice shows what's still owed.
One check paying several invoices? Use Create › Receive payment and spread it across them. It's one deposit, so it matches your bank deposit in one go.
Let the bank do it
If you haven't recorded the payment yet, the bank deposit shows up in Bank transactions with Record payment for the matching invoice. If you already recorded it, the deposit shows Match. Either way the money is counted once.
Removing a payment puts the invoice back to unpaid.