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I go back and forth between a town and route, checking the map all the time till they're on the route, but people have better ways. I recommend a quick ball, or just trying to do a little damage or status condition each turn because any damage on them stays on them.
Dugtrio with Arena Trap or Gengar with Mean Look and Hypnosis are your best bets. I successfully caught both last night by using a Mean Look/Hypnosis Gengar. Level 39 is ideal, as using a Repel, Super Repel, or Max Repel will keep all Pokemon of a lower level for appearing, meaning you will only find Entei and Raikou.
Ideally, you'll want to spam flying to a town such as Cherrygrove or Mahogany and waiting for them to be two routes away. Ideally, if you move to the route between you and your target, it will move to you and be an easy find.
If hunting at night, Dusk Balls are highly effective. Otherwise, stick to Quick Balls, Ultra Balls, Heavy Balls, and Fast Balls.
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