Personally, I moved all of my settings out of customize and into my .emacs file. Mostly because I really dislike the UI for customize.
So, instead of this is my custom file:
(custom-set-variables
;; custom-set-variables was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such instance.
;; If there is more than one, they won't work right.
'(scheme-program-name "scheme")
'(tetris-use-glyphs nil))
I have:
(setq
scheme-program-name "scheme" ; because I like it
tetris-use-glyphs nil) ; it's an example
That being said custom-set-variable does take a number of arguments, one of which is a comment. So you could do:
(custom-set-variables
;; custom-set-variables was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such instance.
;; If there is more than one, they won't work right.
'(scheme-program-name "scheme" nil nil "this is a comment")
'(tetris-use-glyphs nil nil nil "This is another comment"))
The comment will only get blown away when you change the value of the variable, not when you change other variables. I'm not sure that this is the proper usage for this though. C-h f custom-set-variables
has more info.