Revenue Procedure 2002-26.

 If additional taxes, penalty, and interest for one or more taxable periods have been assessed against a taxpayer (or have been mutually agreed to as to the amount and liability but are unassessed) at the time the taxpayer voluntarily tenders a partial payment that is accepted by the Service and the taxpayer provides specific written directions as to the application of the payment, the Service will apply the payment in accordance with those directions.

So the taxpayer just needs to contact the IRS to correct it, preferably with proof of the "specific written directions" for how to apply it.