I had the same exact issue so I started "paying the bills" in batches (jobs for us).  Click off certain bills to pay watching that NO credits are applied - you will have to override that area with a zero every time you click another bill to pay.  Then save and close.  Then go back to that transaction and open it up and start paying more bills within that transaction - when you see the credits on the right hand side drawer you can select one at a time to be applied.  However, make sure you keep a running total and change the "total amount" or it will go crazy and not balance again...  Once you've edited the transaction and added at least one credit to the bill payment they (credits) will populate at the bottom of the screen and it's easier to check off this way.  Very cumbersome but once you get it's not so bad.  Hope that makes some sense & good luck!