Lets assume you have:
CDJ1 to CH1
CDJ2 to CH2
then you just configure whichever deck you're controlling with the 2 F1's to the two free channels.
F1-1 to CH3
F1-2 to CH4.
And all these hook up to your Laptop with USB and I would assume you need a USB hub.
What I think you're confused about (if I am not misunderstanding you) is that the F1's don't have audio running through them. They are just controlling the software. It would be no different if you didn't have them and decided to map deck C and D to the mixers CH 3&4 and controlled them with your mouse.
Hope that answers it for you.