Let me see if I understand this. Sub 1 (S1) will have A left and B left connected as inputs, Sub 2 (S2) will have A right and B right connected.
In each case you will keep the A and B wires separated and they will go to the sub’s L or R inputs?
What you shouldn’t do is connect L A and L B through S1-Left input. That would not break anything but you would lose your A or B switching capabilities. :)
The remaining thing which might cause an issue is if your amp was bridged. That is, if both (+) and (-) were driven, which sometimes causes problems with subs that ground the (-) inputs.