i don't know how important the order really is, but my thinking was this;
skimmer should be first because the highest bioload is in the display and this water is highest in dissolved organics, therfore the skimmer will be most effective there. this region also has a settling area for dense particulates. i also dose my two part in this area because it has the best o2/co2 ratio because of the skimmer
cryptic zone last because if there is a live food benifit the chance of some of it reaching the display is enhanced. the water in this area has one last settling oportunity and microbubbles are completely eliminated. rock covered with drunken bacteria and a mesh bag full of carbon give the water a final polish before returning the water to the display
obviously though with one sump, you'll have to tweek the order to meet your needs, size of skimmer, baffles, and what ever else equipment you have in there