Let me try to give you a quick tutorial:
Start new app -> deploy
Copy index.html from your /deployment/web/ folder to your theme folder. Create a ui folder in your /theme/ folder. Create theme-custom folder in your /ui/ folder Go to bootswatch.com and save the css file in your /theme/ui/theme-custom/ folder (bootstrap.min.css)
Now open your index.html from your /theme folder/ and add the .css file to your header.
<link rel="stylesheet" href="ui/theme-custom/bootstrap.min.css">
This should work, see screenshots below