I have a little different set up than what you are doing but what I have is a tee plumbed in with a valve to where I can run the bags independently or together. When towing especially on winding curvy back roads I have them running independently. It gives a more stable ride and the truck responds better. When running empty or light or on uneven ground I run them together. It allows the rear axle to osculate better and gives better traction.
Personally if I were doing the helper bag set-up what I would do is have one fill but I would put a valve on one side of the tee to separate the bags while in use.