Here is how we organize our MFW materials. I leave them in the box they come in. I plan for all the activities on my computer (I'm trying hard to reduce clutter)
Then when I prep for next day's activities, I take them out and put in the workboxes (yes we do use the workbox method...but...read on)
After we're done with the activities, I put them up on the school board (a large poster board). I like it that we can look at the things throughout the 6 days.
After the unit is done, I take them down and staple them into a file folder. (But my hubby has been telling me a 3-ring binder might be a better idea...I think so too...in the end I did use the 3-ring binder). I also take photos of every thing. After the K year is over, I might take them out and let Ian look through for fun sake and off they go to recycle. We don't have much space for storage.
Now, about workboxes. I REALLY love the idea. Until I buy the separating hanging folders, I'm using this method now. I put everything in "process" (things to be laminated, to be cut, to be prepped etc) in a big file box (we got this from Spore). And then when I prep for next day's lesson, I pull out worksheets (from the MFW box, or from this box etc) and put in a smaller file box. The next day I just take this out and use as needed. It works for us!
We didn't use the workbox at all for the year. We used the very nice form a lady put up on yahoogroup. And I pulled out the sheets into the binder box (for the week) with other supplements I have. And everyday I simply pull out the sheets to use.