I'm sorry, there's no real manual right now.
But using EmChess is quite simple :
Start a new game and enter your and your opponents name and email adress. When you've made your move, you're able to either revert or send your move via the Game menu.
Now your opponent receives an email with some text (you can customize this text in the preferences dialog) and the current game attached. When he opens that attachment with EmChess, he sees your last move and should now make his own.
It's really simple.