Sue says not to alter her system but to use it exactly as she has set it up until you have tried it for a while and then alter bits to fit your family. I highly reccommend getting and reading the book as she explains why she has it set up like she has.
Unfortunately in real life not everyone can afford or has the space to do this first. We didn't and I know there are other families out there in the same boat.
Here are my favourite ideas for tweaking workboxes to make them fit for you.
1 folder per child with 12 sections http://homeschoolcreations.blogspot.com/2009/08/how-were-using-workboxes.html
Using ikea shelving instead of boxes
I just love Cassie's set up - if only I had the room for something like this for each child! http://www.spelloutloud.com/2009/07/workbox-system-set-up-from-cassie.html
Using a drawer system http://wayzleyacademy.homeschooljournal.net/2009/09/28/workbox-system-update/