I created some docs and put them on our wiki. Hopefully they will help and answer some questions. They are works in progress so if you run into issues, give me a shout and I will modify them.
At a high level, we are using Maya to create both the head and skeleton (body) meshes, and the blendshapes and save them as fbx files. We then take the head over to Faceshfit’s client to do the rigging and save the mappings as a .fst file. We do support Blender though and depending on your version and plugins, you can import and export the fbx format.
Our client allows you to specify a .fst file for loading - one for the head and one for the skeleton.
You don’t need Faceshift’s client to create a fst file however, it is just a text file and the docs should tell you how to make it work.
As far as using the SL template, there is no reason it can’t work. Just separate the head and the body. For the body, if it doesn’t have a skelton, you will have to do that. There are some cool tools out there that do that automagically. Check out http://www.mixamo.com/ for their rigger.