there are no major issues, so relax...and enjoy! you own a major great speaker system!
for what its worth, i've also even run my audio aero w/built in pre stage, to my bam, to my amps. with great success!
the differences in placement, in my experience are subtle but noticable, and only you can determine what you like best.
there will be no problem in any configuration, b@m expressed his thoughts on the matter, and I've found his input most valuable. So go ahead and experiment and decide what YOU like best. thats the beauty of the sport.
i should add that I've noticed that when running on 100% battery, when the charge on the batteries gets way LOW the resultant distortion and, what? dc? "noise" is more-so noticable when the bam is between pre and amp...than when bam is in the tape loop or between source and pre. just an observation. obviously, we need to be ahead of the curve and should not strive to let such occurances happen, but...sometimes i've fallen asleep while listening to music etc...
you can't go wrong, and you are the only judge.
great luck and enjoy you great spkrs!