Download the latest Bootstrap source from https://github.com/twitter/bootstrap/downloads. Unpack it to the swatchmaker directory and rename the folder bootstrap.
This can be done automatically by running make bootstrap.
Make your customizations to the two files found in the swatch directory, variables.less and bootswatch.less.
If you haven't already, install LESS to your machine via NPM. More information on that here: http://lesscss.org/#-server-side-usage
In terminal, navigate to the swatchmaker directory and run make bootswatch. The compiled CSS files will be created in the swatch directory.