You can use the command line to generate a theme based off Bootstrap:
codegen theme MyTheme /BasedOn:PJS.Bootstrap
This should work fine. I did have a few issues 6 months ago when I was basing a theme off Bootstrap, I'm not sure if he has pushed the fixes to the gallery, else you may need to get the latest code off his repository.
Note: Also if you read his description, the currently supported Bootstrap theme the developer is working on is actually http://gallery.orchardproject.net/List/Themes/Orchard.Theme.PJS.Bootstrap/3.0.3, so that is probably a good place to get your theme from. Also, if you are running Orchard 1.8 this theme will not work as it runs off .net 4, not 4.5.