IRA early withdrawl payment

The 10% Early Withdrawal Penalty is included on your tax return.  It either increases your tax due or reduced your refund.

The 10% Early Withdrawal Penalty is on Schedule 2 line 6 which goes to 1040 line 15

Then you get credit for all the withholding taken out on 1040 line 17.

so we don't need to make an actual payment to the IRS? It was just billed through our return?

Right.