It could be made a lot simpler if we had our own Moodle Bootstrap Templates styled using the same classes and ids taken from bootstrapbase. Adding a template that is styled for Bootstrap is crazy.
If you want to use a bootstrap swatch in Clean theme the quickest and easiest is drop all the bootstrap swatch css into the Clean's custom settings page provided, which is found by selecting...
Site Administration > Appearance > Themes ->> Click the link names Clean in the list you see at this point.
Add the CSS to the css box and save your settings. You should see the changes directly after you have save the settings. If not Go to Theme setting and enable Theme Designer Mode.
You can then decide whether or not it would be easier to style it yourself from scratch.
I can't get to the page that David linked to. So I am not familiar with whatever Bas wrote or indeed advises.
Hope the above helps anyway.