I have not read Sue's book, nor have I read her website in depth. Most of what I know about the system is based on descriptions and photographs of various workbox systems I have seen across the web. So, my understanding of the system most likely differs from yours and from the original intent.
From my understanding, the system is designed to help children work independently and know what is expected for school each day. One goal of the system is to assist the homeschooling parent work with multiple children, who may all want attention at the same time. This system gives them a way to keep moving forward with their school work without depending on an adult to tell them what to do.
The system works by the parent places the child's (or children's) assigned work for the day in a series of boxes, trays, or baskets and the student works through the trays. Some families have the children work through the trays in order, other families have a more relaxed method and encourage the children to do them in any order they prefer. There are usually tags of some type for the child to indicate that the box is complete. There are also tags to let the child know if it is something that is a "work with me" activity or if it is an independent activity.
Due to our current school space, I could not get a set of boxes or trays for each child. While shopping at the office supply store I found an excellent solution for our family. Plastic folders. The colored ones can hold up to an 8 1/2 X 11 sized paperback/workbook type of book. As you can see in later photos, in addition to the inside pocket with the snap closure, there is a back pocket that can hold several pages.
The clear folders are much larger and can easily accomodate a textbook and a notebook, pencils, and other items. 
Each child has a set of folders, and I have some "family school" folders as well (seen below). The family folders include curriculum/lesson plans, books we're reading together, and any maps, worksheets, or other materials we need.
Each child has a set of clear and colored folders. Kenna's are purple. Inside each folder is the work she needs to do for the day. For example, one purple folder has her math workbook and pencil. The other purple folder has the grammar book, and paper or pencil if we need them for the day. Her large clear folder holds the All About Reading Level 1 materials. That folder can hold the instructor's manual, the student worksheets, and the reader - with room to spare.
I store Kenna's materials on the top of the counter in front of all of her school materials. Her desk usually is covered with projects and toys; so, keeping them with "my" stuff makes it easier for me to find what we need to do. The two stacks are for "completed" and "not completed."
Morgan's books and notebooks are stored in this oversize milk crate. She has pink folders - that hold the work that we do together, and clear folders that are independent work. We often do some of the independent work together, but those things do not require me to be directly involved. At the start of each day, I put the stack of folders that Morgan needs to work on that day out on her desk (or as seen below, on the table). As I rotate between children Morgan can work on the independent activities or do work that is mostly independent. When the other two children are busy with work, I work individually with Morgan.
As Morgan finishes work from a specific folder she puts all of the materials back into the folder and puts it in the crate. This gives her a sense of satisfaction because she can see the amount of work diminishing as she works.
It also provides me a quick visual of how much work she has left to do for the day, and which folders aren't completed. When I look at the stack, I can easily see if I need to work with her or if she has independent work left so I can finish up with Kenna and Moxen.
These folders have the same benefits of trays or boxes because they can be picked up and carried to other areas of the house. If the younger children are being too loud doing their work, Morgan can carry the folder to a different room of the house. At other times, I sometimes pick up a folder and take it and the child to another room to work together.
Each folder has everything the child needs to do the work in the folder (except the math folders that do not have the manipulatives in the folder). So, folders with writing assignments have pencils, paper, books, questions, instructions.
When we do not finish Morgan's independent work in the morning, we just pack them into a bag and take them to grandmother's house. Having the folders helps us to ensure that the work all comes back.
