With the two softwares installed, two independet columns will show instead of just one. "strentgh Jetseat" and "strentgh Sound". Allowing you to assign the strength indidvidually. No need to assign effects on the sound module, use that software just to point to the proper audio output which feeds the buttkicker.
Yes both systems make sense together, because they complement each other. With the kicker under the seat, it will add a new dimension for effects like cannon, chaff, ground bumps, ground roll, landing gear, payload, and especially for things like afterburner or touchdown.
Now you can study adding more shakers for pedal area, I had two there and it´s a nice feeling too, but you need to install them carefully, maybe wired paralel or serial, or using the audio output stereo or surround option.
Enjoy