Lost a long response, short one…

Does the sub amp have a direct input, no controls? Use it. 

Or

Set the sub Amp filter as high as possible, phase 0 and volume about 3/4. If the Sonos Amp volume setting is very low or high tweak the sub amp volume to get both to near mid-range.

In my mind, it seems like it could be problematic if you set the subamp crossover lower than the crossover setting in the app.

ie. if you set the app crossover at 120 all frequencies less than 120 get sent to the subamp and all frequencies above 120 get sent to the main speakers.  If you were then to set the subamp to 80, the frequencies between 80 and 120 would be lost.

However, if you did it the other way around, set the crossover frequency on the subamp as high as possible, then it would play whatever frequencies it is sent from the app and the mains would play anything higher than the setting in the amp.

I have no idea what happens with the phase adjustments.  If you set the subamp at -90 and the app at +90, do they cancel each other out?

You have a 90 setting, not 180? Use one or the other, not both.

Subamp has a knob for zero to 180. 

Zero to 180 - or - zero or 180?

Can't imagine how the first would work, the second is what I have seen.