I am looking at installing this theme in my SF2 project, and I note that there are 4 files at the top of the page to download, namely:
Also read the Usage and Customization sections of the docs at https://github.com/thomaspark/bootswatch.
If you want to use the theme as is (without customization) you only should include the bootstrap.min.css OR bootstrap.css into your HTML:
<link href="/bootstrap.min.css" type="text/css" rel="stylesheet">
Alternatively you can compile your own version of the theme:
@import "bootswatch"
Also notice that Bootstrap adds the autoprefixer for vendor prefixes into their build process. The vendor prefix mixins in less/mixins/vendor-prefixes.less are deprecated as of v3.2.0. So you should add https://packagist.org/packages/bit3/assetic-autoprefixer to your assetic configuration too.