What do I do if fed return was rejected in Turbotx so I paid the tax due thru IRS Direct Pay and now Im trying to file the fed rtrn and it wants me to pay tax due again?

Pick you will mail a check.  Then you don't need to actually mail one since you already paid. You don't enter the payment into Turbo Tax .  Turbo Tax will always say the tax due.  It just the final result of your tax return.  The IRS doesn't update Turbo Tax when they get your payment.

be sure to remove any bank direct debit info, if you don't want to pay twice.

@hogeman37-