Refurb or new? MSRP or best sale price available?
I'd look for Denon 4300/4400, looking at closeout sales as well as refurbs (at accessories4less.com), both have AudysseyXT32/SubEq feature for setting up two different subs; it has been seen at $800 new but you have to watch for it. I'm not sure what you mean by independent subwoofer outputs, or the non-linear thing, but generally you're only going to get the ability to set delay/level for two different subs, they'll be eq'd togethere (and should be).