My libraries are in my Subversion repository (I have just one, which I use for everything), and on all of the machines on which I use Kicad, the libraries are simply checked-out working copies of what's in the repo. The structure of the libraries in the repo is the Kicad default.
A screen shot here:
And here is where they live on a Mac, in the standard locations:
The library table on each machine is identical so it can find the footprints, and the environment variables are set properly. For schematic libraries, the projects are all set up so they point to the libraries.
Whenever I add something to the libraries, I commit the changes back to my repository. When I start to work on a different machine, I make sure that I first update the libraries.