My friend Laura sent me the photo above. I have the same piles. And don't lie. I know you do too.
If you are having a hard time keeping your needles and embroidery flosses organized, you are not alone. I've been confuddled by this forever it seems. Laura wrote me yesterday with this photo and suggested an article on organizing embroidery. I hate to admit it, but though I know of many methods, I never get it together enough to actually do it. Or if I do, I don't keep up the method I tried. You shouldn't be scared by this though. I'm a serial organizer/re-organizer/tryer of new methods. It comes from my inherited condition: most of my family is "organizationally challenged". I know that if I was someone else, I could actually implement these methods and stick with them.
As you can see in this photo, I stash bits in a little box that I just take from room to room with me and in the car. I saw the clothes pin idea (bottom left of photo) one on pinterest and tried it myself. I do like this quite a bit, but I'd also think it's important to write the color number on the pin somewhere. And the brand.
I really love Leanne Beasley's Couch Companion and Project Basket if you want to sew something up for yourself. I couldn't find a US link to purchase it, but I did find one in New Zealand that ships all over the world.
Another idea is take small ziplock bags and punch a hole in a top corner, use a sharpie to write the color number and brand on the top of the bag, and place your small bags on a binder ring . I like these colorful ones from office depot: