This is what I have figured out so far. 

S Corp - 43.071 check box electing to file and pay pass-through and then go to 49.072 and report in 4th installment the pte paid.  

Partnerships - 37.071 check box electing to file and pay pass-through and then go the 43.074 report in 4th installment the pte paid.  

On the front page of the IL 1065 or IL 1120S, there is a box that is marked check this box if you elected to file and pay pass-through Entity tax (I for 1065, L for 1120S).  

What I haven't figured out is how to deduct on the federal side.  Is it deducted on the business return (1065 or 1120S)?  Or do you enter the federal deduction of PTE paid on 1040 and where do you enter it?