A note about the vehicle templates: After you import a template, you should immediately (without rebooting/unplugging anything) File -> ExportUavSettings which saves all settings to a disk file of your choosing, then immediately do File -> ImportUavSettings, SaveToBoardFlash using the same file. If you don't do this, then you will loose some or all of the settings when you power down the FC.
Setup wizard saves the settings into the FC, so you don't have to be so careful about loosing them like with vehicle templates, but it is always good to save a copy on disk using File -> ExportUavSettings if you have put more than a few minutes of work into it.
You can name this vehicle using VehicleName at the top of the Vehicle tab. Press the Save in the lower right and the vehicle will remember it's name (stored in the FC) until it is Firmware -> Halt , EraseSettings'd. The current name also is stored in the file on disk when you do File -> ExportUavSettings
After you have imported a vehicle template or you have run the setup wizard, you customize it with the rest of the settings.
You may change your FMS (Flight Mode Switch), run AutoTune, set up a camera gimbal, etc. Then your settings should again be saved onto a disk file with File -> ExportUavSettings so you can later restore with File -> ImportUavSettings if you need to. This is what I use.
Some (not all?) of your settings, along with notes and facts and a picture, are saved in a Template file in "the standard place" on the disk if you do Tools -> ExportVehicleTemplate -> (fill in the fields) -> Export. Templates you add this way will show up in your ImportTemplate list, but no one else's. If you use SaveAs instead of Export, it lets you choose where to save the file and modify the file name instead of using "the standard place".
I don't know the official way of getting a template added to the global list. That is probably locked down to keep there from being thousands in there.
I am not sure of the status of the template stuff. I think there was an effort made to make sure the current set of templates had been converted for the 16.09 release.
I honestly don't use the template stuff although it's valuable for beginners with a match. Different props or motors and the PIDs won't be as good as they were for the author, and you don't know how good the author was at tuning PIDs in the first place. I always start from defaults. 16.09 has AutoTune (Revo class, not CC3D) in it to make tuning PIDs easier.