A module is nothing more than a folder that contains a ModuleConfig.cfc file. The only requirement for that CFC is that it contains a method called configure(). Modules can also contain models, interceptors, commands, and pretty much anything else you want to stick in them. As long as they contain a box.json in their root, they are also a package, which means they are self-describing, can install dependencies, and can be installed via the install command.
CommandBox has two default modules directories.
~/.CommandBox/cfml/system/modules~/.CommandBox/cfml/modules
The first is for system modules so you shouldn't need to touch it. All the built-in commands are in those modules, so feel free to check out how they work. All user-installed modules are in the second folder. The cfml folder is the "root" of the CommandBox installation, so there will also be a box.json created in that folder once you start installing modules via the install command.
The first way to create a module is to manually create a folder in the ~/.CommandBox/cfml/modules directory and place your ModuleConfig.cfc inside of it. This is the process described in the guide on creating your first module.
If you have a package of type commandbox-modules locally, in a Git repo, or in Forgebox, you can install from any working directory. When CommandBox sees the package type, it will change the installation directory to be the user modules folder.
install /path/to/module
install githubuser/modulerepo
install forgebox-module-slug