When the returns rejected no information is sent to the IRS so they don't know to take out the balance due.
If you choose the paper file then choose that option in the file tab then the correct forms and instructions on how to mail in the return will be presented including a 1040-v for the payment.
Before you paper file try using a single zero for the AGI cuz a lot of the 21 returns took too long to process and the proper AGI is not on file.
