You don't. The game does for you. Every time you finish a battle or something, it heals! But of course, not between turns in battles! (Unless you use recover!)
I know a some: Pokemon Indigo - A little bit slow, but only because it's new. TPPCRPG - Very "Different", I don't recommend this. Pokedox - Not out yet, rumour has it this is going to be the best...
In the Pokemon Roster on the right, click a Pokemon and pick the option "Change to starter". The screen will then automatically change to the Pokemon box. I hope I helped!