You don't have to go in to manual to register the settings - if you do that, when you select C1 or C2, it will put you in manual mode which may not be what you actually want.
Registering to C1 or C2 records the settings that are on your camera at the time, be it P, Tv, Av etc.
I have an old mirror lens that is fixed aperture, and which tends to over expose slightly. As it is fixed at f/8, I also tend to up the ISO when using it. To enable me to use it quickly, without having to think about the adjustments it needs, I set the camera in Av mode and f/8, up the ISO to 400 and dial in 2/3 stop of exposure compensation. These settings are then registered to C1, so that whenever I mount this particular lens, I can select C1 and know that the settings are good to go to get the best out of this particular lens.