For S corporations, Proseries takes the amounts calculated on page 1 of the Form 511 on lines 7, 9 and 13c. totals them and enters them on the Sch K Equiv Worksheet in Section D, line 2.  

The software them allocates the PTE tax amount to the shareholders based on their ownership %.  Sometimes due to rounding, the amounts distributed to the K-1s will not exactly sum to the amount on the Sch. K Equiv Worksheet, so the user will have to adjust the amounts on the respective K-1s.  

One quick comment/question - I am confused by your statement that you are reporting the PTE tax on line 12, code S of the Federal K-1.  Can you explain more why you are deducting it as a flow thru deduction to the shareholder?