Hi,
This would be the same problem for any other binary assets, such as Animations, Prefabs, etc etc.
I usually use categories for my fsm templates, so that they are nicely organized in popups. then, inside the Assets folder, I have always this for client projects:
Assets/App/PlayMaker/Templates/[Category]/[all templates]
what's important is that if you decide to go with a certain way of organizing, you stick to it so that it becomes natural.
Then, On content I want to share amongst many projects, I use Github submodules
submodules are best setup to be rooting at the Assets level, The PlayMaker Utils is a submodule on all my ecosystem github projects.
then when I am in one project, and I make a new template that is reusable, I put it into this submodule, and right from within this rep, I can access the submodule, commit and push that new template, and on other projects, I can pull from that submodule.
that's how I can keep common things in one place only, yet spreaded in multiple projects on my computer or working teams.
Bye,
Jean