Steps
Open the invoice, then click Actions → Manage payments. You can also choose Manage payments from the ⋮ menu on the invoice list.
Each line is one payment:
Date: when you received the money.
Payment account: the bank or cash account it went into, e.g. Chase Business Checking.
Amount.
Add a line for each payment. Customers can pay in instalments.
Check the Balance and Total at the top, then click Save.
See the payment history
Open the Payments tab on the invoice to see every payment with its date and account.
Tips
Paid when you create the invoice? Use Add payment information → Mark as paid in full on the invoice form.
Paid on the spot? For cash sales where there's nothing to invoice, use Income instead.
Bank statement shows the payment? When you reconcile, match it to this payment so it isn't counted twice.