My implementation of Workboxes has evolved a bit, but you might like to look at my blog entries on it. Note that most of them are from early last year when we had just started, and was using actual little boxes on shelves. For a few reasons (largely due to my pregnancy) we lost the use of our little homeschool room and needed something more compact. You can ignore the post on using workboxes with homeschool tracker, as I didn't use homeschool tracker very long at all as I found it too much a pain.
I will answer your direct questions below the link here.
So - what do I put in the file folders? As much as possible, I put in everything that is needed for the assignment. At times, this just isn't possible, but mostly it is.
So, in Delta's box (7yo boy) he had today a file folder with "The Boxcar Children" book in it (to read to me), A folder with "Draw Write Now" and 2 pieces of paper in it, A page of copywork from his handwriting course, along with his paper guide. (He is learning cursive, with large lines.... a page gives him about 6 things to write....), Christian Liberty Nature Reader (for him to read to me), "Great Canadian Lives" for me to read to him, a file folder with a little card in it to do German (our one family topic at this point - it is done on computer, and is in a folder for me to say when it is done.), and a folder with a little card in it for "30 more famous stories) for me to read to him. (I have that book on the Kindle.) For each it is the actual book. I have hanging file folders, and some of the books just sit in between the hanging file folders and aren't actually in a folder. There are hanging file folders that have more of a box type bottom that might be nice to have... Obviously the actual items in the box depend on the day. Occasionally there is a snack or something in it. I also have some cards that say "pick up from station 1" (station 2, etc) for bigger things that don't fit in the box....
Echo (4yo girl) had in her box today: A folder for drawing with 2 papers in it, a math one with her math page and my math teacher instructions. (Delta would have had instructions in his too, but now using the Kindle to read them!) [can you tell I'm loving the Kindle???], 33 multicultural tales to tell, her copywork page (working on single letters - mainly because she wanted too), "A House at Pooh Corner" for me to read to her, and "Our New Friends" for her to read to me.
Other things in their boxes - pencil case with pencils, erasers, pencil crayons, scissors. Delta has the box with the Math rods in it, although Echo is starting to use them too. Oh, they each have a "done" folder too.
I set the file folders up in the evening. I just go on the Organizer, click on show tomorrow's plan, and load them up. I occasionally put in extra stuff - like shoes to practice tying laces etc. When I did boxes, and wasn't trying to juggle so much, I could gather the stuff for the next day during moments while the kids were doing their work, and then they would fill their boxes at the end of the day - but I can't juggle this much anymore! As I keep most of the supplies in one spot, I can fill each box in about 10 minutes, with a bit more time making sure that I know what is going to happen in math and make sure i don't need something extra (like dominoes, or one of the "posters").
Eventually I will have a way to designate folders that they work on alone and ones that they work on with me - maybe the colour of the folder, or a label on it or something..... but right now as mentioned they pretty much all are "work with mom".
This was longer than I meant - but I have to say that it has worked well for our family. If something comes up and we have to go somewhere (like a doctor's office, a car repair place, or a laundromat - all places I've homeschooled!), we just grab the boxes as we go and do what we can while we wait. My son was the type that would have asked "how much more do we have to do?" all the time, and I haven't heard that as he can see it. I'm not tempted to cut out items, or add more in, based on how the day is going. Doing it with the actual boxes instead of the filebox has advantages - it is more visual for them and gives positive feedback as they see the work boxes get emptied etc. It also allows room for projects or a few "fun boxes" - like puzzles etc. And the "creator" of the idea for homeschooling says that there should be 12 boxes, and things should be done in specific ways etc.... but this is what we could do with our living space and budget, and it is working for us!
One liability - it can get to feeling like a task list of things to get through, instead of enjoying each thing....