I sure love your Hello Kitty Cube! And it appears your system is working wonderful for you too
Someone suggested the magnetic bobbin holder called the Grabobbin and I love them! Of course, they only work with my Juki metal bobbins and not my Janome plastic bobbins.. I have several with my threads separated by type/wt like you have. And I just bought a Brother P-Touch for labeling too!
I think the idea of organizing my fabrics, patterns, notions, threads, rulers, etc... into a workable system will be a forever ongoing process! I agree with QuiltE - do what works for you!
Christine