You start use the bootstrap and notice you want to customize bootstrap.This blog show few tips or information about how to customize Bootstrap.
not flexible, not good to maintain.
Very simple to use as online service to customize.
same as above bootstrap-live-customizer.com
edit the bootstrap.css directly (bad)
don't do this.
modify bootstrap project, less, and have your own version of bootstrap source code.
This's good choice, you can customize the bootstrap less variable your self and have version control of it. Whenever new bootstrap comeout, you can merge the latest and build your own bootstrap css.