If you do in fact, get refunded what you expect from the originally filed return, then you're good to go and your check is just paying some of that refund back. If it's not what you expect, then you'll sit tight for that letter from the IRS, so that you don't pay back to much, or end up paying back to little. You'll be able to get everything balanced then, before the tax deadline and only taxes will be involved - not fines penalties and late fees.
