I use a similar technique. For larger parts I use a large plastic tray gardeners use for propagating their plants. About 400mm*200mm by 55mm deep. I keep the instructions in the same container.
For the smaller parts I use a plastic container used for food etc. This sits in the plastic tray.
After I have painted a part these are then returned to their container.
For me this gives easy acess but at the same time keeps everything safe & sound.
Because I’ve just returned to modeling after 35 years, I’m sorting my spare/leftover parts in seperate ziplock bags according to kit/vehicle. I’m putting all of kit figures in a larger ziplock bag.
I’ve started a loose-leaf note book that is tabbed according to subjets for print-outs of on-line references and large protectors for the instructions from completed kits. You never know when the instructions might be needed again and I’ve been collecting on-line articles about WWII German panzer camo schemes. When I find one I like, I print it out and pin it to cork board at the back of my workspace.