While not exactly cheap at $1400 and up, my Onkyo 3007 has separate adjustments for each subwoofer pre-out. Both distance and level can be set manually. I also believe but don’t know for sure that it calculates separate Audyssey curves for each. At least on the initial setup it pings both of them separately. AFAIK the 1007 also does this at about $1200 and up. They are however both processing the same signal as stated above.
I imagine Denon’s less expensive models will also be doing this soon if not already.
The advantage this give me is being able to now change the trim settings on my Buttkicker w/o getting my Butt up and walking over to the amp which when it to five times to get it right would kick my lazy Butt.
