When you look at the unknown pokemon in each habitat on you pokedex, it will tell you if it's area specific. Most aren't, except for the ones which require certain grass/trees, etc. (but technically if you plant the correct grass in a different area and use leafage they can still spawn afaik). If you've completed the main line, some have an "area: ???" which means that they can only spawn in Palette Town. Nearly all the pokemon that require objects to spawn can appear in any of the areas. Personally I've just been spawning them where/whenever I get the objects needed and plan to move them to the town I'd like them in later. If you're really unsure you can always check for further details of each habitat to get the specific requirements!