Organizing my thoughts as I go.
For each directory in nixos/systems/, a nixos configuration is generated in the flake. The directory name should be the corresponding hostname.
Home Manager is installed as a NixOS module (see home.nix and users.nix) and as a standalone configuration.
Similar to the system configs, a home-manager configuration is generated in the flake for each nix file in home-manager/homes/.
The directory name should be user-hostname in order to be imported to the correct system by the nixos home-manager module.
Home manager modules are imported via modules/default.nix.
Within default.nix for both nixos and home-manager, every .nix file is recursively imported.
Modules are put into files with their respective names; and directories are used either for grouping or for additional files needed by a module. Any module that has options is configured via orion.$module.