I always encourage my people to do things the Drupal Way. Even if it is tougher at the beginning, usually pays at the end.
When we started working with Bootstrap we look the "Drupal" way to load the Bootstrap files, what means library style. The surprise was that at the end you need to save the files inside the theme.
A few time later we had the chance to load the files via CDN, but with Bootstrap 3 and the anoying IE8 compatibility we were obligated to install the Bootstap files locally again.
We return to look at libraries compatibility and now found a complex module to do simple things and on version 2.x.x, so we did what we needed to do.
We published a module (https://drupal.org/project/bootstrap_library) that loads via libraries the Bootstrap files installed on /sites/all/libraries/bootstrap, regardless of the theme you are using. It does nothing else.
When using Bootstrap themes it is particulary helpfull to correct Browser Support issues, installing response.js
This module does not depend on a specific version of Bootstrap, it just load the version you install, with the components you install on it, either complete or customize.