Hi there,

For federal, you can enter the amount your client is paying on Misc. Info./Direct Deposit > Miscellaneous, in "Form 1040 payment (defaults to amount due) [Override]"

Not all states will have a similar option, but if your state does, it will be found on the same screen by selecting the state's abbreviation along the top. If not, the client may need to pay online or by mail. 

Rebecca