Special Stages
In order to get a special stage you have to catch three pokemon in one place.
For example: If you catch Pikachu, Pidgey, and another Pidgey in Viridian forest, without getting a "game over", or switching to somewhere then back again, a hole will appear saying "Go To BONUS". Go in and you will be in the stage.
The Red field Bonus Stage is Diglett's Cave and the Blue field Bonus Stage is Meowth's House.
Where to find Pokemon
Each Pokemon has a preferred hiding spot. HEre's where to find many of them.
RED FIELD
Pallet Town: Charmander, Rattata, Nidoran (M), & Poliwag.
Viridan Forest: Weedle, Pidgey, & Pikachu.
Pewter City: Spearow, Jigglypuff, Ekans, & Magikarp.
Cerulean City: Oddish, Mankey, Jynx, & Abra.
Vermilion City Seaside: Shellder, Krabby, Ekans, & Farfetch'D.
Rock Mountain: Voltorbe, Diglett, & Mr.Mime.
Lavender Town: Gastly, Magnemite, Cubone, & Electabuzz.
Cycling Road: Spearow, Doduo, Lickitung, & Snorlax.
Safari Zone: Paras, Rhyhorn, & Chansey.
Seafoam Islands: Horsea, Staryu, Seel, & Articuno.
Cinnabar Island: Ponyta, Growlithe, Omanyte, & Kabuto.
Indigo Plateau: Machop, Onix, & Ditto.
BLUE FIELD
Viridan City: Squirtle, Nidoran (M), & Bulbasaur.
Viridian Forest: Caterpie, Rattata, & Pikachu.
Mt.Moon: Zubat, Paras, & Clefairy.
Cerulean City: Bellsprout, Meowth, Jynx, & Abra.
Vermilion City Streets: Shellder, Krabby, Farfetch'D, & Sandshrew.
Rock Mountain: Diglet, Voltorbe, & Mr.Mime.
Celadon City: Mankey, Meowth, Eevee, & Porygon.
Fuchsia City: Magikarp, Goldeen, Kangashan, & Exeggcute.
Safari Zone: Doduo, Nidoran (F), & Chansey.
Saffron City: Ekans, Sandshrew, Hitmonchan, & Hitmonlee.
Cinnabar Island: Ponyta, Koffing, Aerodactyl, & Magmar.
Indingo Plateau: Geodude, Ditto, Moltres, & Mewtwo
Note: There are more Pokémon in each area but those are the ones you will find most often.