I sort mine by Store and then designer. I have started then making sub folders within each kit and sorting by Papers, Alphas, Elements, Frames, etc. This is especially helpful with the Colab kits, I think anyway.
I have recently started copying all of the files into sub folders of just Papers, Elements, Frames, etc. because I like to do the speed scraps and it makes it easier if you can look in one place for papers, etc. I have been watching though to make sure that each file name in those sub folders have the designer and kit name so I know who to credit to. It is taking a while, but that's just personal preference for me.
Love to hear more about how others do their files.