Does it only appear at certain times? And I don't remember the PokeNav sprite at the bottom left flashing blue.
It doesn't appear on the PokeNav.
It appears on your Pokedex. After you see it, go to Lati@s' Pokedex page on your Pokedex, and hit "Area". It should highlight what Route it is in.
Source: Experience
After you beat the elite four, since you have Sapphire, Latias will appear randomly around Hoenn. You'll just have to go searching for it around in grass. If you have a master ball, save it for Latias, because when you meet it in the grass, it'll flee right after you attack it. And, you'll have to get it REALLY weak before you can catch it with a regular ball, and that means you'll have to track it down. To track it, just look it up in the pokedex and click "area". Make sure you don't fly to that area, because if you do, Latias will fly somewhere else. Bike or walk there. If it's too far, then just continue on with something else in the game and wait until you bumb into her again, or keep checking its position every once in a while. Good luck!
Source: http://answers.yahoo.com/question/index?qid=20081206145016AAtCtcV
