Sequence of custom-set-variables and Evil init

I'm not sure whether to place the custom-set-variables call before or after initializing Evil. Some customizations only work before Evil initialization, some after. For example, (custom-set-variables '(evil-overriding-maps nil)) doesn't work correctly if after Evil init. (custom-set-variables '(evil-search-module (quote evil-search))) doesn't work correctly if before evil init. Which way is it supposed to be? If I leave them separated, Emacs consolidates them into one again when I use its customization interface.