No. Once you encounter them once, you can open your Pokédex and look inside the location data you will see where it is, and track them from their.
After you meet it 12 times, it will rest at the Sea Spirit's Den.
EDIT) So I never explain why I say No. From Personally Experience and from Recent Research, If Zapdos is on the route your on, it should be the first Pokémon you encounter.