It is a weird process for sure. Typically you want to create your projects using a template that does not refer to a shared audio pool of a different project. Also you want to always store projects in their own new folder.
Here is how I do it.
- Create a template that does not refer to a different audio pool. Basically there are two ways to do this.
If creating from an existing project (probably most typical):
a) - Make sure the project is saved.
b) - Hit the “Backup Project” and save it to a different folder location. This saves a new project with audio that is not shared with the old project (not sure why Steve Helstrip says the “Backup Project” function is broken as it is currently working for me).
c) - Close the original project and open the new “backed up” one.
d) - If applicable, delete all audio from the Pool.
e) - Make all other changes you want the new user template to have. Save the project.
f) - Now hit “Save as Template” and provide a descriptive name. Once saved this template will be listed under the “More” tab in the right side of the Steinberg Hub.
g) - After creating the new template I usually trash the backed up project I created it from (but you don’t have to).
If creating from a new blank project (probably not as common) you would not have to do above steps b) through d).
- Start your new project using the project assistant from the Steinberg Hub:
a) - Make sure the “Prompt for Project Location” option is enabled.
b) - Pick the template you want from the list in the “More” tab.
c) - Double click the template name or just select the template and hit “Create”.
d) - Go to the folder location where you store your projects and hit the “New Folder” button.
e) - Name the new folder then hit “Select Folder”.
f) - Once the project opens I immediately save it using the same name as the project folder. I got into this workflow habit to prevent loosing the new project when I mistakenly closed it without saving it.
That’s it… have fun. 
And yes… I submitted feature requests to fix the create template mess.
Regards 