Well, the thing is that when you repoint them, you'd have to repoint them to free space so the new table can be expanded. This obviously will take a megaload of space, so a good course of action will be to expand the ROM itself (this also means you'd have to switch to APS from IPS).
After that you may customize the new everythings, and add the data you need to add. Then of course, after doing all this you can put in the stuff onto the game itself. Keep in mind that you'll have to hex edit to add new Pokémon, as A-Map does not support the expanded tables and stuffz.