HTML5 Boilerplate and Twitter Bootstrap

You're exactly right, it is a template. It's a template which brings together a set of best practices for developing HTML5 websites. You don't have to use it but if you do you can rest assured that you are building on a solid foundation which has been developed and honed by top developers over the years. In the words of Paul Irish, one of the principle developers of the project:

“It’s essentially a good starting template of html and css and a folder structure that works., but baked into it is years of best practices from front-end development professionals.”

I would suggest downloading the fully commented version of the boilerplate and reading through the code to give yourself an idea of the thought which has gone into it and the cases it handles. (See also this article which highlights code snippets from the boilerplate which you should be using on your site). These should help you decide whether you want to use it as a starting point for your project or not.

The HTML5bp initializr even includes a bootstrap option, so it couldn't really be any easier!