So let's say you want Ho-Oh for example.
1. Make sure the coordinates are for the Red Wormhole
2. Make sure you unset Flag 4 (not the species number. Literally flag number 4)
3. Make sure you set the other numbers 1 through 15, except 4.
If you're still having difficulties, I don't how else to explain it.
thanks! it worked perfectly, this is my first time using this tool and I didn't knew about that function, this makes it a a lot simpler, now I can finally fill up that pokedex