Pokémon Model Ripping Project

[Charmaleizard]

So, I'm still quite new to this...I tried to load a render of the greninja, bulbasaur, venusaur, etc. models in ohana3ds, and a majority of models have irises that are layered on top (above eyelids).  How do I fix that texturing?

Also, what program is needed to compile Sun/Moon character parts?  Again, I'm fairly new to this and I'll try the best I can.  Do you somehow link the parts to the animation block in some way?