NetSuite bank reconciliation won't work for us - what other options?

We have a unique situation when it comes to being paid.  We bill insurance for our customers and we will receive a check from the insurance company that might pay 500 different customers.  We process payments in an external application that creates the payments in NetSuite via web services.  This all works great and with the volume of checks and payments it's the only way we could post payments without hiring and training 5 more people just to accept payments in NetSuite.

Now we have a problem with reconciling.  We have our bank statement which shows deposits and checks but of course it doesn't show the individual deposits for our patients.  What we're trying to do is group all the payments on the reconciliation form by check number, then adding them up and reconciling on the statement.  This is an INSANE amount of work and VERY error prone.