MiniDSP 2x4 HD
That's the correct set of things you'll need to integrate multiple subs, especially multiple subs with radically different capabilities (MBM is a mid-bass monster), VTF-15H Mk2 are just plain monsters all around).
Q1. Don't know, don't use Audyssey myself; I'd hope it can tell you if the phase needs adjusting, but I'll have to defer to someone who uses it. Without a way to measure, you're not in the best position to judge phase. (REW & UMIK help here). However, an SPL meter and the test CD that comes with the subs will help you. The output should be 6dB higher with 2 subs. If it's not, then they're out of phase with each other (if they're both set the same and stacked, they should be in phase). When you've got them in phase with each other, then you'd use the test tones (warble would be best, IIRC), around the crossover frequency and your SPL meter to get the highest reading by flipping phase on them and seeing what it does (setting to best integrate with the main speakers).
Q2. Not sure how the MBM gets hooked up, but with just the 2 VTF's, you'd want to use one output to each VTF if they aren't stacked together. If you go MiniDSP, then you'd run everything off one output to the MiniDSP. If you run both VTF's stacked, then you should be able to use a Y splitter to them since they'll effectively be 1 sub. I don't know what audyssey will do if the MBM gets hooked to one output and the pair of subs to the other, since the MBM, to the best of my knowledge, is a 50Hz and up sub, so auddysey might screw things up when it sees a sub that does little below 30Hz and a "sub" (VTF pair acting as 1 sub) that should go down into the teens with authority.
Q3. Absolutely, you can stack the VTF's. If stacking the VTF's, you'll get about 6dB more output than a single VTF, and might as well use a Y splitter to drive them since they're effectively 1 sub when stacked from an acoustic standpoint.
Q4. personal preference.
Q5. Depends on if you can integrate them properly.
I'd recommend a MiniDSP 2x4HD, UMIK-1, and REW and then not stacking the VTF-15H Mk2 together as a general rule. However, you may have the 1 in a 100 room where the spot the VTF's are going to go results in flat bass, and if that's the case, then stack them up for more output! But you've got to be able to measure to know.
MiniDSP 2x4HD, UMIK-1, REW... The holy trinity for running multiple subs.