Right now, I only have one of everything. So it definitely helps me keep track of it! If I lose anything, I'm in trouble!!
As for thread, I still haven't started using anything different for piecing vs sewing, so I just organized it all above the machine on a rack, and by color. (There are a few thicker 'utility' type threads that I use for certain hand sewing projects, but they're easy to spot right off the bat!)