See Twitter Bootstrap Customization Best Practices regarding customization and LESS with Twitter Bootstrap.
In general, I wouldn't recommend directly modifying your bootstrap.css file, because it will make it difficult to edit in the future if/when the core css is updated by the bootstrap folks. Instead, just have a second style sheet that is referenced after the bootstrap css. Add your overrides/modifications there, like so:
<link rel="stylesheet" href="css/bootstrap.min.css" media="screen"/>
<link rel="stylesheet" href="css/my_styles.css" media="screen"/>
Of course, for performance, consider combining these and serving them as one to reduce your http requests.