The best thing to do is.
1. fork twitter-bootstrap from github and clone locally.
they are changing really quickly the library/framework (they diverge internally. Some prefer library, i’d say that it’s a framework, because change your layout from the time you load it on your page). Well… forking/cloning will let you fetch the new upcoming versions easily.
2. Do not modify the bootstrap.css file
It’s gonna complicate your life when you need to upgrade bootstrap (and you will need to do it).
3. Create your own css file and overwrite whenever you want original bootstrap stuff
if they set a topbar with, let’s say, color: black; but you wan it white, create a new very specific selector for this topbar and use this rule on the specific topbar. For a table for example, it would be <table class="zebra-striped mycustomclass">. If you declare your css file after bootstrap.css, this will overwrite whatever you want to.