Yes, as other replies have pointed out, at least part of the excessive bass heaviness which you're experiencing may be due to possibly having the M100s and the sub "doubling" the bass. If you have the M100s set "Large", the crossover setting is meaningless and they play full-range, along with the sub in the lowest bass(if you have the 4308 set to also use the sub on music, with a "LFE + Main" setting).
Set the M100s "Small" with a crossover of probably 60 or 80Hz, and let your excellent subs handle the lowest bass which they do best. Also, make use of Audyssey.
