Save as both a preset and track template then! I've yet to have any problems with templates myself though.

I can't say I have noticed any problems with track templates.

Crashes on import are one I get quite a lot. Messing up synth assignments is another.

Projects vs Presets:
 
This is from EZ Drummer 2 and I think it is the same idea for SD2:
 
SAVING/OPENING A PROJECTSaving a project saves everything in one go. Any changes you have made to the LibraryPreset and any arrangement/editing made in the Song Track will be saved with the project.To save a project, you can use standard procedure “Save” or “Save As” from the File menu(standalone only), or you can use the main menu in the top right corner.

I created a folder on my secondary drive for my custom kits for SD2. Use the Save Project in Superior, point SD2 to the folder that contains your custom drum kits, name the kit and save. You can load the kits from that folder as you choose.
I have individual folders for each drum library in the custom kits folder so it is very easy to find what I am looking for. As far as Splat and SD2 are concerned, Splat remembers the drum kit settings in the project but you will need to set a template if you are starting from scratch on a new project.
I use both methods but I always save my SD2 kit in my custom kit folder in case I ever need it again.

I'm not at my DAW but I believe that Scook and Kylotyn are correct.  I use the Load/Save button at the top center to save the entire kit.  It gives you the option to name each saved kit.  This also saves any mixer/FX settings inside of S2 that you may have.  True, it's not very well documented.
 
HTH

I feel foolish for not even noticing the Load/Save option. I think I will do both, save the kit and keep a template.
 
Thanks to all!