If your subs are powered, then the speaker level inputs will go to a line level converter before going to the sub’s plate amp. This will present a high impedance connection compared to your mains.
Speaker A output to R/L mains and Speaker B output to R/L subs should be no problem.
Folks use dual mono subs driven off a sub or preamp out so they can position and adjust the subs to null out room nodes. For many systems this produces better results than true stereo subs. Lots of reading on this subject is out there.
A another consideration is high passing your mains to 1) better integrate with the subs and 3) take the bass load off the mains. I use this approach with great results.
good luck and enjoy