If a Customer is set up on a Payment Plan and decides to pay in full or pay in advance, you have several options you can choose.
Option 1 - Let the system do the work
When a Customer makes a payment that is over the amount in the current Invoice(s), it shows up as a Credit on the Transaction History. This is true whether or not the payment is attached to a particular Invoice or if the payment is just on the Account (not attached to a particular Invoice).
If there are any Future Invoices (i.e., from a Payment Plan) on the account, then when those are billed, the Credit on the account will be applied to those Invoices.
Option 2 - Reconcile the Account manually
If you don't want to wait for the system to do the work, you can reconcile the account yourself. Here's how:
Step 1 - Create a new Invoice. This support article describes the steps to create a new Invoice.
Step 2 - Pay the Invoice. See this article for how to pay an Invoice.
Step 3 - Delete Future Invoices. This article describes how to delete a Customer's future Invoices.
Step 4 - Turn off Auto-Pay. It might be a good idea to turn off the Auto-Pay on that Customer's Account just to be sure their Account is not charged in case a future Invoice was missed. See this article for how to turn off Auto-Pay.
The account should be balanced after taking those steps. If it's not, please reach out to support via the chat.