Well, what you can do is to start a new project, using whatever project template you want to start with and want to change, make all of your changes, and then save it as a TEMPLATE, in the Project Templates folder.
I did this for the Normal template, to split the console off to my second display, and to load up a couple of soft synths I always use, (Kontakt and Battery 3), and that way I get my standard custom kit and all of the assignments for each drum to separate tracks, and levels and such, and the same for Kontakt, with some standard instruments loaded and routings and all of that. (Piano, organ, bass, strings). I can swap out instruments in Kontakt as needed and still have everything routed just the way I like it.
When I did the above, I did not overwrite the original Normal template, I just saved it under a new name - Normal - Split. That is completely a matter of personal preference, you have total control.
Templates are wonderful, just remember to change the file type to Template, so that it saves it as a project template instead of a project, and also make sure you navigate to the Project Templates folder so it will show up in the list with the rest of the templates when you are creating a new project.
Hope that helps,
Bob Bone