As we raid dogs and have too too many in the house and live on sugar sand, I have all thread stored in plastic containers with tops, last two I got at connecting threads on sale for $9.99 and 2 sides, all material in containers from Wal mart with snap lids, that way stuff stays cleaner when dust gets going.
http://www.connectingthreads.com/too...___D82068.html
Wish I had more room to get mor organized but this works for now, along with a set of poly shelves from Wal Mart to hold some stuff, thread someplace else. Kind of like you, scatter here and there.
Enjoy your new space and good for you.