If I understood your post correctly, you have things setup the way you want and want to save those settings as a project template. You have attempted to accomplish this, but the 'template' you created shows up as a project and not a template.
IF my understanding is correct, it sounds like you saved your settings as a regular Project, rather than a template.
IF that is the case, here is the fix:
1. Open that Project (that you are wanting to use as a template)
2. Click on File>Save As
3. When the Save As dialog box opens, you will need to change the File Type from Project to Template, AND you will need to save it in the location Cakewalk uses for Project Templates. If you did not alter that location, the default folder location for Project Templates is: C:\Cakewalk Content\SONAR X2 Producer\Project Templates. So, in the Save As dialog box, navigate to the above location, and since you changed the File Type to Template, you should see all of the existing project templates listed
4. Now click on Save - your project template will be saved in the same place Sonar looks when it generates the list of New Project Templates when you either open Sonar or click on File>New.
I hope the above made sense, AND I hope my read of your post was correct.
Please post back and let me know if this helps you,
Bob Bone