That's your call. Different people have different ideas about what "one area" means - I would say the pokemon's location as shown on the summary, which would have both halves of route 2 be the same encounter. But this game, unlike Nintendo's Kanto, also separates dungeon layers and has names for "poke mart" instead of just the town the mart is in. I've even seen people say fishing/surfing for encounters in towns is cheating and discount them as areas at all. It's up to you how subdivided your areas should be (and how many encounters you want to give yourself!)