You're adding a PKMN which doesn't exist in the third generation games, right?
If you are, then there is a way to add some without replacing the existing ones, I think...
There are 20+ blank slots after Celebi and before Treecko. Those blank spots can be used, however, their cries, by default, are Unown.
But there is another way to add a new PKMN without replacing any other which are currently existing, but I have no slight idea how to do that.
But I know the guy who has accomplished that though, so you are probably better to ask him instead of me. =/
This is his thread, by the way. He already locked and discontinued the project, 'cause he switched into FireRed.