You might want to check this thread out:
In short, you can but expect changes at some point.
home-manager can fully replace GNU/Stow and similar tools and I would highly recommend it.
The nice thing is that when you have the package defined in home-manager as well, the config can live right next to it.
Like for my Emacs config, where the config files live right next to the home-manager config and get symlinked to the correct place by home-manager:
https://git.2li.ch/Nebucatnetzer/nixos/src/branch/master/home-manager/modules/programs/emacs/default.nix#L123
BTW. for a nice setup you probably don’t want to use nix-env but rather define everything in home-manager.