Well, while you are contemplating spending more money take a look at the REL subs which offer independent separate volume controls for the inputs which allow for one set up for stereo and another for LFE. Or, you could buy a matching sub as the one you have and set the player to "no sub" and run one sub for each channel. For instance, left channel to sub and then out to main left speaker. With this though you'd have to be able to hopefully direct the rear and center bass to mains.

I'd try a typical HT set up first before anything where the sub crossover is bypassed and use the crossover in the player, setting the Maggies to "small" Hopefully, this will play a 2.1 for you in stereo.

An odd thing with my SVS, when I had the Velodyne I didn't get bass from the sub in stereo but with the SVS I do. It's great. The only thing I can imagine is maybe the 2-channel signal was too weak to turn the Velodyne on. That doesn't seem likely but I didn't change anything on the preamp. Another thought is the SVS plays higher so therefore I hear the bass with the SVS.