wash off your makeup using whatever cleanser you are using to follow the regimen. If you use makeup that doesn't wash off easily, some people use the makeup wipes first but they can be a little too irritating to your skin in the first couple of months of following the regimen. It may be better to change the type of makeup you use or even try to go foundation free for a while.
Good luck!
I find that the cleanser that comes with the Regimen doesn't get all my makeup off, so I remove my makeup first with my Shu Uemura cleansing oil and then cleanse with my usual cleanser.
Although the cleansing oil is very gentle (and I highly recommend it), I still try not to wear makeup unless I have to, because the extra rubbing/washing that it requires is going to add some irritation.
the neutrogena "one step gentle cleanser" is supposed to be both a makeup remover and a gentle facial cleanser, and i absolutely recommend it. you can use it over the sink, but i like to use it in the shower, just because i splash a lot haha, and basically you just get your face wet, pump the cleanser into your hands and lather it up, and then gently rub it all over your face, then rinse off as usual!
i rub it over my eyes very gently if i'm wearing eye makeup, and although it doesn't usually get all the makeup off my eyes, it helps a lot. after my shower, i just go in with an oil-based makeup remover on a cotton ball or q-tip and wipe off the excess.
the one step gentle cleanser comes in a little blue bottle with a silver-colored pump, if you're looking for it. it's very inexpensive (you can find it at most drugstores) and i really think you should give it a shot!