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If the only pokémon you want in the game are the Johto pokémon, edit "pokemon.txt" in the PBS folder. Easy.
If you want both the Johto Regional Dex and a National Dex, look at this response to my question about Regional Dexes. Note that you'll also have to do something else to make the player able to switch between the Johto and Regional Dexes, which could be anything from making it dependant on where you are at the time to flipping a switch to unlocking it with a password - we can't help you with this aspect until you decide what you want to do.
Also, this is a question about Pokémon Essentials. Don't make your own thread for a question that belongs in the thread that exists solely for questions about Pokémon Essentials.