I wasnt aware you could tailor the debit amount for more than the amount shown on the return when paying through the software.

I agree with Terry, just use IRS DirectPay and make the payment for however much you want to pay.

Theres always a chance that the IRS computers will automaically refund the overpayment if the the IRS hasnt computed the penalty on the amount due yet (It doesnt happen immediately at the time of filing), so if youre paying the penalties ahead of when they've been assessed, this could happen.   

I generally let the client wait for the bill from IRS then pay the penalty/interest balance due.