I cloned Zach Holman's (holman) dot files implementation[1]. Mine [2] is basically Ian's torn apart and put back together (so i could understand it). It consists of symlinked rc files, and env and private_env files which get run at login / profile boots. The private env stuff (passwords, api keys, etc) are cloned from my home server or from encrypted Dropbox folder (still figuring out how I want to handle that)
I've done the same thing, I've customised holmans dotfiles and just replaced the content with my preferences. I really like the rake mechanism for symlinking. Simple and convenient.
1: https://github.com/holman/dotfiles
2: https://github.com/pfarrell/dotfiles