The estimated payments the program puts out is ONLY to keep you from having an underpayment penalty if you pay the estimates timely, file the return timely AND if you pay any balance due on the return by the original filing deadline (not any extensions). Sending in the estimates will not guarantee you will not owe on the return ... it is only to keep you from having underpayment penalties.
The IRS can access an underpayment penalty + interest, a failure to file penalty + interest and a failure to pay penalty + interest. The TT system only helps with the first penalty and will compute an estimate underpayment penalty on the return based on your entries of any payments you made and the dates you made the payments.
