I think that I'm getting the hang of how to deal with Project Templates. Especially the creation of them.
I have created one default template (assigned to one default project) and when I want to create a new PT, I load the default one first. Then I save it under a new name.
Lots of settings will be inherited this way. Then I create a new project, using the new PT. While the new project is open, I create new glossaries and memories or assign existing ones. Then I group, dock and arrange all resources the way I like.
That's it. When I quit CafeTran Espresso, everything will be saved automagico.
Speaking about my default PT: I have one default PT for every language combination and direction.