Here's what I did:
1. Count them (every division if it's your case) and make a list of what you need/want to put in them. This is to get an idea of how much space can you spend and how you are going to distribute themes in shelves. If you want to make an outline of your shelf it will help you.
E.g. My "office" shelf is 5x3 (which equals 15) with two closed drawers, which are perfect for those things that always look messy. And I needed to store folders, books and notebooks, a printer, art & crafts material, wrapping supplies, fitness material and miscellaneous stuff boxes.
You might know already where you need to have some things. In my case, for example, the printer is exactly where it has to be, not just because I'm used to it, but because of wires also. In the same way, books and some folders are also in the right place. They can already be included in my scheme.
2. Think of what you need most and the most reachable places from where you are used to be.
E.g. In my case, this shelf is behind my desk and I'm closer to a determinate area. To me red area is the less reachable and the other areas turn more reachable as the colors turn darker.
3. It's time to start playing. Begin matching colors of the outline with the ones on your list.
E.g. For the darkest green I have folders, books and some paper supplies. Well paper should be near the printer, which gives me 2 options (A,B) but it's easier to have them in A zone. Keep going like this until you get an idea of what you want. Think that it's not definitive. You can change stuff while organizing.
(You can just write down what you want to put in every place, I drew it because I would write in Spanish plus my handwriting is not really understandable, as you can see in some places)