Normally, one would take these downloaded files and put them into their own web application directory tree. However, there is a better way. Unless you are planning to use this on an Intranet with limited Internet access, you can use a copy of these files hosted on a “content delivery network (CDN)”. A good example of this is the jQuery library hosted on Google’s CDN. Google has a number of hosted libraries on their network. This has several advantages, one of which being caching. If everyone is pointing at a common hosted library, that library gets cached on the end-user’s machine instead of being reloaded on every site that uses that library.
While bootstrap is not hosted on google, there is another CDN running on CloudFlare called cdnjs that provides a lot of the “less popular” frameworks, including bootstrap. Here are the URLs to the most current version of bootstrap files (they have version 2.0.0 through 2.1.1 currently).
Here’s an example you can use on your own.
Finally, I found that NetDNA also hosts bootstrap on their CDN at [www.bootstrapcdn.com]. I would say that either CDN would be fairly reliable, as they are both sponsored by their CDN they are running on. One advantage of this site is that they provide a lot more than just the basic bootstrap hosting such as custom themes and fonts.
To use them, you can simply swap out your css and js scripts.
UPDATE: I added jquery into the above examples because several parts of bootstrap rely on it (such as the Modal dialogs).