Well, at the risk of being called OCD or crazy, Here's how my mum and I have our cross stitch supply area set up.
I usually just pick out what I need when I'm working on a project, if I need more I go out and buy extra and put the remainder back in the box. We use a checklist and once a year when this really keen local shop has their superbowl sunday sale, we stock up on anything were missing/ new colors.
All our extra pieces we keep in a small box. We just started this a few months ago because we were running out of room in the big shelf thing and taking out the pieces really helped.
Now, I know someone mentioned about not being able to hand pick colors because everything is in number order. This is what I use. now, It must be from the 80s or something, because my mom claims she bought this when she first started cross stitching when she was preggers with me and I've never seen one for sale. If anyone knows where I can get one, a replacement or one with updated colors I will marry you right now.
I hope this helps, Honestly 80% of this is my mom being a crazy organizer, I could never keep up with this by myself, If it was up to me, It would probably all be in a lump in the bottom of a shopping bag.
I'll add the PDF of the shopping list we used this year too ^^