You have two choices since the system didn't process the estimated taxes correctly.  First choice have them send in the payment with a 1st Estimate payment voucher.  Add a note of explaination that ProSeries did not handle the estimated taxes correctly.  The second is if you have EFTPS set up as a CPA and have individual user accounts and send in the 1st Qtr and all future quarters.  That's what I had to do for my personal taxes.