Load AP161 with Separate Payment & Remit to Document Express

We are working on implementing Wells Fargo SPS solution for healthcare vendor electronic payments. The process uses the remit file of the AP161 only, so we have our cash code set up to do a separate payment and remittance file. For our own records, we would like to be able to have a human readable copy of the payment to attach to the invoice for archiving. We use Document Express for check printing today, and it does a good job importing the AP161 as long as the Payment and Remittance are combined. I have asked MHC about this and they are researching as well.

Has anyone found a way to import the payment and remittance files as separate file (similar to an overflow file)? Or do I need to create a process that will combine the files together (matching the 2 record from the payment file with the 3 record of the remit file)?