Using post Gen 3 Pokemon in my hack, need help

[GallowPole]

I have been wanting to make a hack using pokemon from Gen 1 to 6 using FR. Having no experience in Pokemon hacking and doing the leg work to add the Fairy type and everything from Gen 4 onward, when it has been done in the past, is a waste of time. So I have been opening many hack with all the new stuff and found one that works without errors in the Gen3HackSuite and AdvancedMap (801 Pokemons).

However, trough my experimentations, I have found that AdvancedMaps "Wild Pokemon", Advanced Starters and Advanced Trainer do not include Gen 4 and future Pokemons and do not work on any hack with future pokemon.

How can I modify these 3 tools to recognize future pokemons or am I to use other tools I do not know about. Maybe my method of using a completed hack with Phy/Spe split and Fairy type already done is broken.