I bought some thread holders at Wal Mart and couldn't get any more so got some from connecting threads. I label and store by colors so when I want a particular color I look at boxes, grab the right one, have lots of thread in colors from sewing clothes etc. Have a box of button/craft and quilting thread. Keeps it clean and bobbin stays with spool and labeling makes what I am looking for as I have a very small 6-8 sq ft. to store everything and have to have it organized. Material in labeled bins is in same place. Doesn't make it easy to sew sometimes but do what we have to.
To make it easier I have two small clear sterilite 1.2 qt. containers (5 x 7)from WM to store colors I use a lot, makes it easier as we have puppies right now to reaching thread is harder. You have to find a way that works for you and keep working on it. Would just love having a sewing room but don't so make do.