I don't think there is a right and wrong way to customize emacs, whatever works is good. What I do is have a .emacs and my custom elisp files in a Dropbox folde

I don't think there is a right and wrong way to customize emacs, whatever works is good. What I do is have a .emacs and my custom elisp files in a Dropbox folder. Then I have a simple ~/.emacs file that loads the Dropbox one. If I didn't use Dropbox for various other purposes I think I'd use git as well.