Yes to all of your questions.
You need to assign the MIDI messages coming from the GC Pro to the preset numbers in your Factor Pedals. Refer to the Factor's manuals (in fact, I think both pedals have almost identical MIDI options, hence the operation should be the same).
It's actually pretty easy to set everything up once you get the idea of assigning MIDI Program Change numbers to preset numbers.
You have to set your MIDI output of the first Factor pedal in the chain to "through" first, so the MIDI signal can be fed to the second Factor.