I've been using CPT only for a couple of weeks now. I find it a very useful program. I'm looking forward to the next release because, although I've come to accept the limitations of sub-repertoires, I don't like them :)
I play a lot of blitz chess on FICS. I use BabasChess, which allows me to journal all my games in one PGN file. I can then go over them later, finding novelties, with CPT. When I find novelties that I've played, I discard them. I do this because usually what I play as a novelty is unsound :). When I find a novelty my opponent plays, I analyze it with crafty and try to find a reasonable answer which I then learn as a line for next time.
I try to weed out any options in moves that I would make so that I only have one move to learn for a given position. This makes it easier to learn more positions, and they don't all look the same.
I've divided my sub-repertoires into several of my favorite opening lines, but I still have a few catch-all sub-reps, black and white, where I put openings that opponents have played, but that are not that common. When I go through my sub-repertoires, it is like playing all the openings I've faced on the internet and answering them with the best move.
I think this use of CPT is pretty effective. It has probably added 20-30 points on my rating in the last couple of weeks using it, as I'm not losing in the opening as quickly anymore. But this is where I get back to my title. How do you use CPT?