If you separate PNRs, they can reconnect them and its a PITA. They can also not reconnect them and simply note that you are traveling together. Your call...
My thinking is separate the PNRs IF...
This is a Medallion heavy route with lots of gate lottery upgrades regardless of the flight time (Sat is a little easier).
Determine what's most important to you and go from there. From your post, my total guess is free/priority baggage checking and sitting together. You can do both pretty easily.
Best of luck to you and the non-elite!^