Customizations are saved to the file specified by custom-file, as
calls to custom-set-variables and custom-set-faces.
When you save customizations, the current implementation removes the
calls to custom-set-variables and custom-set-faces, and
replaces them with code generated on the basis of the current
customization state in Emacs.
By default custom-file is your .emacs file (for GNU Emacs
and older XEmacs) and is custom.el in the same directory as
init.el (in XEmacs 21.4 and later). If you use another file, you
must explicitly load it yourself.
As of XEmacs 21.4.7, when custom-file is present, it is loaded
after init.el. This is likely to change in the future,
because (1) actions in init.el often would like to depend on
customizations for consistent appearance and (2) Custom is quite brutal
about enforcing its idea of the correct values at initialization.