You will need to pay in the extra $99 since the original debit you authorized was just for the original amount of tax you owed. So, send the voucher in with a check.
Let's back up. If you filed and got accepted then added the 1099 INT you should have done an Amended return on a 1040X. I don't know if the 1040X is ready yet so you might not be able to efile it. In fact, You should not amend or change your return until you get the refund from the original return or your payment has cleared.
The amended return will only be the difference you get back or need to pay. You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your original refund amount and line 21 should be your additional refund. If you paid on your original return it will be on line 16 (but don't include any penalty on 1040 line 38). If there is an amount owed with the amendment, it will be on line 20.
Go by the actual 1040X. Line 18 should be your original refund amount and line 22 should be your additional refund. If you paid on your original return it will be on line 16. If there is an amount owed with the amendment, it will be on line 20.
Ignore the 1040V and the new 1040 . That is for the original return or what the original return would have been if it didn’t need correcting. Don’t pay the amount on the 1040V.
Okay, so I'm understanding that I did this completely wrong. And I should instead fill out a 1040X? Would I still need to fill one out? I do not believe this would make a, significant impact to my return as they amount on my 1099-INT was $16.75.
If your first original return was Accepted then you could not have efiled another return unless it was an amended 1040X return. I see the 1040X is available now. Maybe you were still seeing Accepted for the first return.
You should probably take out the interest and put your return back to the way it was when you originally filed. Then try amending the right way.
How to Amend the current year
https://ttlc.intuit.com/turbotax-support/en-us/help-article/tax-return/amend-federal-tax-return-current-year/L7eS6o1qh_US_en_US?uid=lfunevhk