(Here are the Jekyll Bootstrap docs on themes.)

First, visit https://github.com/jekyllbootstrap and choose the theme you wish to use and fork it using the "fork" button (on the top right). There is even a theme explorer where you can preview the available themes.

Then clone the repository to a directory of your choosing:

git clone https://github.com/USERNAME/theme-the-forked-theme.git

Set the remote repository:

git remote set-url origin [email protected]:USERNAME/theme-the-forked-theme.git

Make any changes you may wish to make and commit them:

git commit -am "My changes."

– push the changes to Github:

git push origin master

Then go to your jekyllbootstrap repo and do:

rake theme:install git="https://github.com/USER/theme-the-forked-theme.git"

Done.

I'm not as of this moment sure of how to elegantly update the theme in the Jekyll Bootrap repository once you have commited changes to the theme onto Github. For now I'm going with removing the theme files and then doing the theme:install command above again. Like so:

rm -rf _theme_packages/the-forked-theme assets/themes/the-forked-theme _includes/themes/the-forked-theme
rake theme:install git="https://github.com/USER/theme-the-forked-theme.git"