The old wiki contains a post about how to add Handlebars support in a project, but it's outdated. I didn't know where to put an update (as the wiki has been merged into Yeoman.io) so I posted an entry on my blog instead.
If you think this instruction should be part of some FAQ on Yeoman.io - feel free to use the material.
And thanks for a great tool!
I'll close as I believe this is not really relevant to the way Yeoman evolved. This should be documented on specific generators offering support for Handlebars.