I found my second magic plant last night. Yay!
I have found seed organisation quite difficult. I too keep a handy "bottom row" of my highest seller.
I was keeping two of every seed I got (one to cross-breed, one for backup) but I don't have enough space for that now.
My research program is based on finding the flower and plant combinations rather than breeding specific plant species, so I now keep 2 of each discovered flower and plant type.