I think storing things by stacking is always a good idea. Not only does it help with keeping like things together, it also saves space—mainly because shelves are usually far enough apart that a stack can easily be accommodated. I also like to use containers that are the same; it helps me quickly identify what’s inside at a glance.
For example, I put all my pins in plastic boxes called ‘Really Useful Box.’ I purchased mine at Staples for approximately $1 each. They’re available in different colors and sizes so you can probably find a box to fit your needs. Selling features include: stacking nicely, hinges that insure securely attached lids, transparent plastic, durability and affordability.
I also like to use storage units that are unique and fun. I received this wooden box as a gift and the first thing I thought was how it would be great for storing thread!
By luck, the compartments are the perfect size for both sizes of Aurifil spools as well as other brands, and additional odds and ends too.
I hope this post helps with your storage needs, or at least helps spark some ideas!
Note: I am not endorsed by any product I have mentioned in this post; they are just items I like, use and wanted to share information on.