On the master page, I use the Head HTML code webpart and simply add a link to your stylesheet in there.
<link href="/CMSPages/GetResource.ashx?stylesheetname=YourStyleSheetCodeName" type="text/css" rel="stylesheet"/>
This example is using a stylesheet created in the CSS Stylesheet app, if you want to use the bootstrap css, you can link to the local copy Kentico offers or use one in the cloud, simply change your url.
Same is true for your JS files. In the same webpart or add a new one, simply add
and you're set.
This way you don't have to worry about IIS loading CSS files when you don't want and you can still use the out of the box functionality.