In angular-cli.json you can change the app configuration.
If you want to add ng2-bootstrap for example:
npm install ng2-bootstrap --save
or yarn add ng2-bootstrap
In angular-cli.json just add the path of the bootstrap at node-modules.
"scripts": [
"../node_modules/jquery/dist/jquery.js",
"../node_modules/bootstrap/dist/js/bootstrap.js"
]