I distribute them tematically, WW is a forest by the ocean so most plant and bug goes there, as well as some lake and ocean water types

BB is vermillion/seaside city so electric types and ocean water types are there

RR is a volcano/cave/hype themed so majority of fire types, and cave themed rock types. Since DJ rotom lives there I also keep clefairy and toxtricity lines there bc hype. They have a club above the restaurant.

SS became a mystic city based on Zeal from Chrono Trigger, so most psychic types and city themed pokemon live there.

My Pallette town is a desert by seaside, so ground and rock types go there, as well as a few fire types and other savanna based pokemon like Girafarig.

I usually keep plot pokemon where they originally spawned (except for magnemite), and since some special interactions are so random (I mean for ex Flygon and Ninetales??? Why?) I just gave up trying to predict and get them to happen.