Start with the Template sample to learn how plugins work and use it to generate a new project for you to start from.
With Cordova 5.0, plugins are now hosted in NPM, and we have published our plugins there as well. Follow the instructions in the readme for the plugin you want to add. It's as simple as typing
cordova plugin add cordova-plugin-bb-app
on the command line while in your project directory, to add the BlackBerry 10 App plugin for example.