When I used REW for my system with dual subs, I started with just one active. Once I got that dialed-in the best I could, I then added in the second one. This way, if there were any phase issues between the two subs and somewhat the mains, I could correct it easily with a phase adjustment on the 2nd sub, volume adjustment, crossover adjustment, positioning adjustment in the room, etc.
Had I tried to do everything at once, I would have been chasing my tail not knowing where the problem was. Bass adjustments in room are tricky and when adding multiple subs that might cancel one another out at different frequencies or create peaks and nulls it gets much harder to find problems.