Upgrading from MAX BR1 MK2 to MAX Transit

I currently use a MAX BR1 MK2 with a 5 lead Poynting antenna on my roof. I am purchasing a MAX Transit (single modem) and cannot change out the antenna at this time. Question: How should I connect my TWO Cellular antenna leads? One on Main and One on AUX or BOTH on MAIN and leave AUX open at this time?

Depends. If you want the best chance of using two operators at the same time I would connect your roof antenna to the two MAIN ports and leave the included stick antennas connected to the AUX ports. However if you tend to use a primary provider the most I would stick the roof antennas into MAIN and AUX for that modem and use stick antennas on the other modem.