You're over thinking it. In practice it just doesn't matter. Barring some unforeseen truly mismatched gear that is.
Let me show you just how little it matters. My integrated tube amp doesn't even have a pre- or sub- out. So I made one. Disconnected one unused RCA input, re-wired to connect speaker output to it, put a couple resistors across it, hooked it up to my two Dayton sub amps. Works beautifully. Read my threads. Awesome, mind-blowing bass, articulate and tuneful and deep and 3D as can be.
A 5th sub, powered Talon Roc, runs daisy-chained off one of the Dayton bypass outs. These same components have been compared running 4 subs off one amp, 2 and 2, and 2 and 2 plus one. Stereo and mono. There is no stereo low bass. So that's another one you can dismiss.
As far as settings, the biggest most common mistake by far is worrying about phase. Phase is a total red herring. Not because it doesn't matter at all, but because the way so many imagine it works is so misleading. Phase isn't about timing, like it needs to all be time aligned, like it needs to be for midrange on up. Phase is about modes, reinforcement and cancellation. Phase is about smoothing and/or extending bass response.
So what you do, set your 4 or 5 or however many subs asymmetrically around the room- different distances from you, the room corners, and each other. Play music and listen. Mains run full range. Adjust sub crossover and level to as smooth and even transition as you can get in that range. Make very small adjustments and listen to different recordings. Not all recordings have great low bass.
When it starts to get close you can try adjusting phase, or location, of one or more subs. A phase shift is nearly identical to a location shift. It is identical in terms of how it interacts with the other subs. It is different in how it interacts with the room itself. So not quite the same but the exact same in terms of what you hear, which is best thought of as EQ. This part is really time consuming since now you are listening for smooth even balance across low bass frequencies that just don't come up that often on many recordings.
Personally I did all this but didn't put a lot of time and effort into the phase/location steps. By the time it got to that point it really was feeling like splitting hairs. Ninety-plus percent of the improvement is simply running 4 subs. You get another 9 percent with position, level and crossover. By the time you get around to phase you're so close to perfect that if you're still at it I can only tip my hat to you.
