I wouldn't stress to much about the templates. Just look at them as visual reference material for different platforms, and game mechanics.
Personally I like to start off by creating a blank new project then if I can't remember whats all needed for a certain platform, or type of game mechanics I look through the templates, and examples for what I need.
As far as a rule of thumb goes first consider the types of devises that you want to market, and all there different screen resolutions. Ask yourself do I want the game to fill the screen completely on all devises, or will I be happy with black crop bars showing depending on each devices resolution? I wrote a little something about this here:http://www.scirra.com/forum/multiscreen-cocoonjs_topic61313_post376578.html?KW=#376578
For example I have been working on a Windows 8 game, and last week I decided I wanted to also make an Android version. As far as the code changes went all I really had to do was add the WebStorage object, and convert all my Windows8.Roaming info. This is were commenting your code well comes in handy.
But when I tested my game It plays, and looks well on high end quad-core 7 inch, and larger devices like the Nexus 7. But on 800 x 480 resolution smartphones the player, and sprites are so small it's unplayable because I built the game at a 1368 x 768 resolution. If I would have built the game for the smallest resolution device that I wanted to market 800 x 480 it wold have worked on all resolutions. Lesson learned :)
So I guess another good rule of thumb is to always build your game to the smallest resolution you want to market first.