Well, for this, let's go to the official site:
>In Pokémon Omega Ruby, Latios will approach you to join your party, while Latias approaches you in Pokémon Alpha Sapphire. And it has been discovered that Latios and Latias can also Mega Evolve!
Bulbapedia says that the [email protected] is holding its mega stone.
Now, for the Eon Ticket -
The official site says that
>Players with the Eon Ticket will be able to go to Southern Island again to encounter and catch Latias in Pokémon Omega Ruby or Latios in Pokémon Alpha Sapphire.
I assume that they are, again, holding their respective stones.
EDIT: Apparently you get the second stone from your mother in Littleroot Town.
The Eon Ticket must be received through StreetPass.
So, in summary:
No, you only get the Eon Ticket to get the legendary not in your game. When you get the first legendary, it will be holding its mega stone.