@nanounanue The one way to use rde is generating home-environment record object, which you can pass to guix home reconfigure, so basically it doesn't matter too much if you craft home-environment from scratch or using rde or combining both approaches.

If you talk about your current hand-crafted ~/.config/emacs it will be backed up to home folder by symlink manager: https://guix.gnu.org/en/manual/devel/en/guix.html#Declaring-the-Home-Environment

If you have ~/.emacs.d - move it out manually to other location, as it have priority over ~/.config/emacs.