Do you remember when Entei and Raikou was running about they moved to different places in Johto? Ya same in this case but its going through both regions. The best was to encounter is is to go through a place suck as Goldenrod City where there are no gates and you can check your pokegear to see if its near. Keep checking until you and Latios are on the same route. Oh and it doesn't have Roar or Whirlwind but it will run away.
Hope it helps :)