Hi Ti, Very nice work.
The q-sys looks very capable. How many taps, at what sample rates, can it handle?
One trick I've learned for aligning subs, when using linear-phase crossovers, is to find the sub's delay with everything in play other than the FIR filter. This usually gives a dead-on repeatable time. Then turn the FIR filter on, which has a known # of samples delay, add that delay to the previous measurement, and you get a specific delay that ties linear-phase together pretty perfectly. Delay finder times will group very closely around that total time, the more linear the phase of the sub and main through the crossover region, the tighter the grouping will be.
Of course, if you are using IIR between sub and the DIY you will have to go through the 'phase trace overlay method'. Which can be a little confusing at start because of inconsistent delay time readings for the sub.
I'd recommend to anyone who has the FIR capability to first learn to tie things together with linear-phase, because it becomes trivially easy with a little experience. It is also good preliminary training for moving to IIR and the phase trace overlay method , for when the FIR latency is too much for the application..
FWIW 
