I was not aware you could get a payment plan when filing an extension, since the final tax due was not yet determined. Assuming that is what you did, then your payment plan notice should have information on how to make additional payments.
Failing that, you would file your tax return and pay the amount owed. The IRS might make one extra monthly auto withdrawal before they catch up, but they will eventually return it to you. The IRS will also adjust the final amount owed for interest and late fees.
