The most elegant and native way to manage dotfiles across your home directory and subdirectories is using a bare Git repository.
While you could move all your configs into a single folder and create symlinks (the traditional approach), a bare Git repository allows you to leave all your files exactly where they are. It requires zero extra software—just Git—and prevents your home directory from becoming a cluttered mess of symlinks.
Here is exactly how to set it up.
A bare repository separates the Git database from your working tree. The database will live in a hidden folder, but Git will treat your entire home directory as the working tree.