CommandBox can be extended by modules installed from external locations. When you install a CommandBox module, it will automatically be placed in the correct modules location (inside your CommandBox installation) regardless of where you run the install command from.
Later, if you want to view, uninstall, update, or otherwise interact with these system modules, you can just use the standard package management commands, but add the --system flag to them. Any time you add that flag, the current working directory will be ignored, and you'll be interacting with the core modules installed into CommandBox.
The package commands that accept a --system flag are as follows:
package install
package uninstall
package outdated
package list
package update
package show
package set
package clear