How do I ask Emacs (Aquamacs, in my case) to make backups not only of the documents I work on, but also of customization files such as customizations.el?
In addition to the backup configuration that Dualinity has described, I'd suggest you put all your emacs customizations under version control (git, hg, bzr, etc.). Many times I've needed to revert my customizations due to unintended side-effects. Reviewing changes you made from six months ago is trivial if you check in all your changes as you make them.