The way it works with integrated two subs using an SHD is as I'll describe below. It's not automated like DLBC but not 'goofy' in that it very much does work and actually this functionality is the number one reason I've used miniDSPs for several years now.
The SHD has four independent output channels, which can each have their own time delays, crossover filters and other DSP. To integrate two subs with two main speakers you use measurements made using REW to decide on what the appropriate time delays, crossovers filters and (rough) levels are to integrate the subs with the main speakers. This then produces a 'left speaker' which is the left main speaker plus sub(s) and a 'right speaker' that is the right main speaker plus sub(s). Then you run Dirac Live and it behaves exactly the same with these combinations as it would as if there were two full-range speakers. So here you get the advantages of Dirac Live for controlling the combined frequency response and phase adjustments to improve the impulse response. What the stereo version of Dirac Live doesn't do (but DLBC does) is to do the initial subwoofer delay and crossover optimisation.
In my own system I have integrated a single sub as above but it can be down with two as well. MSO can also be used when two subs are used.