Since Pabluez's answer back in December, there is now a better way to customize Bootstrap.
Use: Bootswatch to generate your bootstrap.css
Bootswatch builds the normal Twitter Bootstrap from the latest version (whatever you install in the bootstrap directory), but also imports your customizations. This makes it easy to use the the latest version of Bootstrap, while maintaining custom CSS, without having to change anything about your HTML. You can simply sway boostrap.css files.