Yes... and to take this a little further...
Generally the Bose Way is to take mediocre drivers, and make them somewhat presentable with extensive processing. Based on the OP's original symptoms of rattling grilles and flapping speakers but little sound, I strongly suspect that there's a brickwall HP filter for the entire full-range signal in the tops, and by aux feeding the subs you are bypassing that protection. I would run the system as designed.
The signal path is designed to go from mixer to subs to tops when using the whole system, so any limit/EQ/Crossover processing for the subs is
in the subs, aux fed or not. My preference would be to reconfigure the system as "non-aux fed" for at least a few gigs to see how it performs, but ultimately I'm not in charge of the rig so it's not my call.
Patrick if you getting better results now, that's great. But I don't think there's any way this system is going to give you the sound you are looking for from your 5 and 6 string basses. If the distance is too far to transport your subs, you'll just have to roll with it. Best of luck...
Agreed. Rolling has commenced.