If you have svereal thousand chips this may not work for you, but with just 2000 chips this works great for us. We have a set of chips labeled in red from 1 to 1000 and a set labeled in black from 1 to 1000.
To store and organize the chips we have a board for each color set. Each board has ten rows of ten slots that hold ten chips each. The slots are roofing nails that are long enough to go through the board and support ten chips with some room to spare. Each slot is labeled with the number chips that belong there.
If all ten chips are returned to the board they are placed black side forward. If there is a chip missing, they are placed orange side forward. With this method we can look at the board and very quickly see what chips are missing. This comes in handy after a big meet when we are check to see if all chips have been returned.
This won’t work for everyone, and it takes up more space than putting the chips in the boxes they came in, but for a manageable number of chips it’s great for organizing.