I store mine separately. The spools are standing in little organizor baskets by color. The bobbins of regular sewing thread are in the organizers tha Nancys Notions sold- like 3 tubes together. Bobbins snap in, stored by color and ina basket. Embroidery bobbins are in a bobbin box as are my quilting bobbins. Emb. Threads and quilting threads are stored in separate places in my pattern file cabinet's top drawers. I also write a "Q" on my quilting bobbins with a Sharpie so I don't get them mixed up. The same with my embroidery bobbin thread.