Amount i should pay after amending my taxes?

I filed my federal taxes early and received a refund. However I just received a schedule K form 1041 which shows a capital gain amount, I just finished amending my taxes with TurboTax. I now owe some money. My question is does TurboTax have any way of knowing that I received a check from the federal government and should that refund be added to  what TurboTax now says I owe?