Paid too much by ignoring amount submitted with requested for extension

[Quahog]

I submitted my final federal tax on 10/16 but did not deduct the amount that I had previously paid when I timely requested an extension in April. Last night I mistakenly paid $3968 instead of the $968 which was the amount that was owed following the amount submitted for the extension ($3000). Is there any way to make sure that the IRS takes payment of only the $968 amount? If not, what do I do?

[rjs · Accepted solution]

The best thing to do is probably to just wait a while. I expect that the IRS will take the $3,968. Then at some later time they will notice that you overpaid and send you a refund for the excess. If that doesn't happen, you will have to either file an amended return or contact the IRS to straighten it out.