When I started on my project I created a /css directory and then a /twitter folder underneath it full of the raw .less files. When I decided I wanted to use a bootstrap component, I would move it out of the /twitter folder into the main /css folder and then include it. It's a good way to get a lot out of Twitter bootstrap without falling into the "obviously bootstrappy" look.

Over time, I've tried to remove what I can of the bootstrap look and feel but I found it hard (for me and my below average css skills) to beat some of the items (forms, etc). My site (http://www.thetaboard.com) is definitely 'built with bootstrap' but I don't think it gives off a 100% bootstrap vibe.