Working with Twitter Bootstrap is no different than working with any other frontend framework. In this case, you do not need to keep css by default if you are not going to use it. Just change your layout to include css / js files, as usual, and create your elements so that Bootstrap expects you to do this.
However, since no one likes to reinvent the wheel, I would suggest using the CakePHP plugin, which handles everything for you, here is one
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