Pretty sure it's supposed to be each move has one use per thread, though don't quote me on that, especially since I'm not sure if most players have more than one restoration move per character. Most just rely on berries and other items due to commonality.
As for damage/health, it's an honor system. Of course if you're a level 5 Treecko going up against an Arcanine, your best bet is to run. When you encounter Pokemon using the dice, just try to think how your Pokemon would fair against the opponent at their weakest state. As for your energy, it's simply a tool to keep you from rolling an you can interpret it as you wish. Some people simply stop rolling when they hit 0 energy and have their character go on as if nothing happened. Some people make their character become tired, sluggish, and need to catch a breather. And then some people go so far as to have their character faint as if it were directly linked to health.
If you keep reading through the rules most things should be answered, and going through the rest of Questions and Help might allow you to find more answers and clarifications.