Answer:
It's like catching Latios and Latias in Pokemon Ruby and Sapphire. After you've met them in Ecruteak, Raikou and Entei will appear on your PokeGear. When you catch up to them, make sure every time you meet them you either weaken or put it to sleep, poison it, paralyze it etc (sleep will still run away) over time it will be weak enough for you to throw balls at it, just go nuts.