The SUBWOOFER output from the FBQ carries the low-frequency information in the range specified on the crossover knob. However, this output is considered an "extra output" - and it's crossover settings do not filter out the low frequencies from the main channel outputs.
To clarify, changing the crossover setting for the SUBWOOFER does not affect the channel outputs. Changing the LO CUT filter settings on the front panel of the unit, however, will affect the SUBWOOFER output.