so it sounds to me like we'll possibly be getting the set up for how she ends up on Earth-1 in Supergirl, but the actual main part of the overarching plot will then begin in The Flash
Yep, seems that way.
Oh well, at least they have room to go bigger next season with a full 4-part crossover story
To be clear, I love crossovers. If they did a Flash/Legends of Tomorrow crossover and left out the garbage I'd be happy. But, even if I liked either of the other shows having four crossover episodes for one story is ridiculous, and really making someone watch episodes of four different shows to get one story is a bit BS, even if all the shows were good.