Hey, I don™t see any issue wearing makeup while on the regimen. It really depends on how your skin is tolerating the products and whether there™s excessive dryness and or flaky skin. The regimen can definitely have this effect so I suggest moisturising  prior to any makeup application. The use of a sunscreen can be really beneficial as well. If your skin is tolerating the products, there™s no issue wearing makeup, just make sure to remove it  

For makeup removal, I suggest either a makeup removing balm (the body shop has a nice one) or an oil cleanser. Once you have removed the makeup follow with an actual cleanser......cream cleanser, gel cleanser, whatever suits. Try and be gentle with your skin, no excessive rubbing. If you have active acne, this can really aggravate the skin and cause further inflammation. Hope this helps! 

They recommend not wearing foundation, but that was impossible for me with how bad my skin was (catch 22, lol). I used mineral foundation and made sure to keep my makeup brushes clean.

Definitely you should wash any makeup brushes at least once a week. And be sure to avoid touching your face. I know, the minute I say that, that's all you want to do.

Another thing to think about is not touching your face without washing your hands. This means even while applying makeup. I wash my hands before I apply moisturizer, before applying foundations, and usually one or two more times as I realize I am about to touch my face. This has really helped.

And, as mentioned, be gentle with your skin, no excess exforliatingor scrubbing. Only wash your frace twice a day and moisutize to keep it from drying out and producing excess oil. This sounds weird, but too much washing dries out your skin, and cause it to produce more oil, which in turn can affect your acne.

Regardless of what some might say, you can wear makeup with no problem; just make sure the makeup you are wearing is light and non comedogenic. Also, to make sure your makeup does not cause acne be sure to deeply and gently clean your skin every single night, and also make sure to wash your makeup tools once or twice a week. Personally, to take of my make up, I massage unscented mineral oil on my wet face making sure to thoroughly massage the oil well enough to breakup my makeup. Once I am done massaging, I apply a pump of my gentle cleanser on top of the oily-makeupy mess. It is important to make sure you go over all the area you previously massaged with oil. The cleanser step makes it easier for you to rinse off the oil and makeup without having to scrub your skin.
BTW, the best type of make up for acne prone skin is mineral makeup. The zinc oxide in mineral makeup is not only sunscreen but also anti-inflammatory, both of which are great for acne.
Hope this helps.