To quote Karri Saarinen, Designer at Kippt, advice on customizing twitter bootstrap.
Not everyone is a designer, but to customize Bootstrap you don’t need that much. Changing some background colors and fonts will go a long way. It really isn’t that hard or take that long, and it’s well worth it.
Tweak button styling. Personally I’m not a huge fan of the default button styles. Good thing is that changing some gradients and shadows isn’t that hard. (Bootstrap Buttons http://charliepark.org/bootstrap...)