I don't think you need to stray away from makeup. I don't wear makeup myself so I can't say how good the acne.org moisturiser is as a makeup primer. Also, I don't know how good the cleanser is at taking off makeup so it may be a good idea to use a makeup wipe or a cleansing oil of some sort to take your makeup off before hand.
It's all trial and error so really it's up to you what you want to do, maybe go makeup free for a couple weeks and see how your skin tolerates it at first.

If you can put up with going makeup-free, it's better, plus fewer products to apply meansfewer steps in the morning, saving you time. The Regimen works best if you only put Regimen products on your face, and if you wait till you're clear before introducing other products/steps. But it's really up to you, many people treat their skin successfully while wearing makeup.