This post is a long time in coming. I don't feel "qualified" to give advise on homeschooling, but I've always been an organizer. I have my messy piles around (all over right now), but I do enjoy planning and organizing. This has been our first year homeschooling, and I have a ton to learn... but I thought that someone may glean an idea or two from how we set up our school this year. So here it goes...
I'm writing this to a My Father's World user (since this all we know), and again it's for teaching only Kindergarten (again... this is all we know, so far!!).

This is our "School Cabinet". It was a Target buy, years ago, and perfect for all our supplies. I outfitted it with drawers (also from Target). The bottom cabinets hold all of our arts & craft supplies. There are bins for colored pencils, one for paints, one for glue - tape - glue sticks. One compartment on the very bottom holds the boxes of extras that came in the deluxe package (ant hill, butterfly garden). In the top of the cabinet we store our "daily" stuff. Drawers that hold our Cuisenaire Rods and Rods Alphabet book, textured letters, preschool bins that came with the MFW preschool package, a roll of the ever handy contact paper, and my "teacher's file boxes". At the very top of the cabinet are horizontal paper holders which house our construction paper. Really my "go to" item daily is just the one green lidded file box in the top cabinet. Here it is:

In it are two hanging files. One of which houses the things we use sporatically: Blend ladder chart, Bingo game cards, extra calendar pages, etc. The other hanging folder houses the manila folder for the unit with all the worksheets in it, our 100's chart and calendar page, Lucy's
awesome Kindergarten Daily Schedule (from the MFW-K Yahoo group), and my Teacher's Manual. In the front of the box are our jars with our 1's and 10's sticks in them, our flashcards, a ziplock with the textured letters we've learned to date, and teacher's pencils, stapler, eraser, etc. (stuff I use everyday). This box is all we need for school most days. We've gone for camping trips where all I need to do is grab this box, and we are good to go. I store the other unit manila folders in an additional box, pictured here...

The folders are put in order of the curriculum and as I find things that I can use for that unit I just stick it in the appropriate folder. If we happen to have books around the house that go with that unit, they go in here too. I've torn out all the worksheets and also put them in the right folders. I put sticky notes in the folders several weeks before the ant and butterfly unit so I remember to order the critters. I also put in notes about special things we may have done for that unit that may come in handy in two years when we repeat K with my daughter.
When we get to the end of a unit, I simply take the 100's chart, calendar page, and my Teacher's Manual out of the current unit's manila folder, and I file that folder back into this box. Then I take the next unit's folder out of this box, and put in in my "school" box : ). Easy peasy!!
My kids each have a box of their own too. They are the same as my box, but in it are their school supplies (pencils, dry erase board, their badges for the week). When it's time for school, I just tell them to get their school boxes and the three of us sit at the dining room table and go to it. By the way, my daughter (3 years old) has coloring books, and some MFW preschool items in her box, as well as some age appropriate worksheets to keep her busy when I need one-on-one time with my son.

I've noticed some posts on the MFW board asking what mommies do with all the worksheets once they are completed. What is working for us is a large 3", 3 ring binder with page protectors. (You'll see this in our cabinet next to my file boxes. At the end of each unit I put the worksheets for that unit into his "K Binder". My son loves to show this off to people, and it's a great reminder to me of how far he's come this year. As for the "stuff" (art projects, etc.) that don't fit into page protectors, I either put it in the pocket in the front of the binder, keep it on display around the house, or it goes into his school box (for now).
One other important part of our school day is our "book basket". Quite literally a basket... Not required in Kindergarten, but this is where we house the books we've found around the house that have to do with our current unit. The "bag" in the basket houses the books we've checked out from the library on our unit. A cozy corner that I can send my kindergartner to when my 3 year old needs one-on-one time with her "school".

I hope this helps someone. More than anything, I pray that other mommies that are using MFWK for the first time are as blessed as I've been this year. I would love to hear other ideas too that may be helpful, as well as ideas for years to come...
Thanks for reading - Amy