That's correct, they perform separate functions. What does your current regimen look like? What moisturizers are you using? Are you Lye or No Lye relaxed?
I purchased both of the same products myself on Saturday. I used the Roux PC Shampoo and Conditioner and my hair feels much smoother. I did not use the Aphogee with it (I was planning to as well) because I a bit intimidated by what I've heard about it. I tried to find some info online about using the Aphogee and Roux PC together but found nothing. Have you used Aphogee before with success? If not, I would recommend Nexxus Emergencee Treatment. It's not as hard core as Aphogee and I saw great results from it.
I suggest you use the whichever protein treatment first and see how that works. If you're satisfied I would then go ahead and use the Roux with a Moisturize DC on your next wash day.