If I have stitched from a kit, I don't tend to keep the leftovers. I do keep the pattern though in case I wish to stitch it again. Then, I either convert to DMC floss or just pick colours from my stash that work. While I stitch the kit, I place the floss in individual snack size baggies (from the Dollar Store) with the colour number as per the kit marked on the baggie, on a piece of painter's tape (so I can get it off easier and reuse the baggie). Getting more frugal as I contemplate retirement!
If I have stitched from a pattern, all floss is wound onto bobbins (yes I'm a bobbinator!) before I begin, then once done, the bobbins go into plastic storage boxes in numerical order. When I begin a new pattern, I look over the pattern to see usage of the various colours, then pull from the boxes if not a lot of it is needed. Large amounts of one colour are purchased at the time to keep the dye lots the same.