I organize colored legacy plant storage the same way I do the plants I sell:
by Flowery, Leafy, and Desert Plants. The legacy plants divide up nicely into these three groups. Each plant holds 8 seeds, if I need more than 8 plants for some reason (I only stock 8 of each at a time) I can grow them for 10 days to get a seed off each one, or 11 days to get an additional seed. One of the plants I grow always goes in a special bag as a seeder, so I grow this one all the way to replace the plant I took for seeds.
For plain legacy plants I have 9 boxes that hold 2 of each of the plants, this is the first row:
Inside each bag are the deco mode plants so I can replace the ones on the vendor quickly, on the outside are 4 seeder plants so I can grow a lot if needed.
For the new plants I throw seeds in bags organized by seed type, I don't keep too many since storage is precious. For the colored new plants I will put a book in with the plants holding the seeds since I'm still only partly done growing all my seeders in that area and don't want to screw them up by accident.