You can use plugman command to install/uninstall custom cordova plugins.

To install plugman

 npm install -g plugman

Install plugin command syntax:

plugman <install|uninstall> --platform <ios|android|blackberry10|wp8> --project <directory> --plugin <name|url|path>

Example:

plugman install --platform ios --project platforms/ios/ --plugin plugins/cordova-plugin-test/

For more plugman options check this link