Second, SooperLooper works in stereo just fine.
Third, you can use some sort of MIDI controller to fade the loops in and out. It's pretty easy to map a control to a parameter. You can use something small, like the Korg NanoKontrol or the Akai LPD8 (both work over USB, very simple to use). The parameter you're looking for is "wet" for each loop. So if you had a LPD8, you could map the buttons to record/overdub for each loop, and use the knobs to fade loops. Just pull up the MIDI mapping window, select which loop# you want to effect, pick the "wet" parameter, click "learn" and move the knob you want. Nothing to it.