This is a little confusing. I select the option in "preferences" to "use per project folders".
I always open a template I created, for new projects.
I then have to create a new folder.
After tracking to the template, I rename the project and change it to a .cwp and change the location to the new folder I just created.
This is not difficult, but there have been times I have forgotten to follow the steps exactly and then had a mess to clean up.
I wish it was a little more automatic, or maybe there is a way, and I am not aware of it.