Get your taxes done using TurboTax

Thank you!  I do owe quite a bit for the Premium Tax Credit.  Should I simply pay that now or would that just confuse the IRS since I've paid all other taxes owed?  So for example, let's say I owed $40,000 (and paid it) on the 1040 that was filed and accepted but without the 8962.  Then I added the 8962 in TT and owed another $10,000.  If I make that $10,000 payment what will the IRS do with it since there is no 8962 and an updated page 2 of the 1040 that shows the additional $10,000 for  PTC?