Finally we decided we would get a big cabinet from Ikea and just homeschool mostly in the dining room only we didn't want it to look too much like a school room so here is our solution:
Here is my super simple organization to make my son a tad more independent. If I say - lets do math - he knows which one to grab and it is all in there. His Math U See manipulatives, his DVD and his workbook and a pencil. I got them at Target for $4.99 each.
Here is what the shelving looks like all together.
And I put the maps up in the boys room. We do have to walk from the dining room to the boys' room to do any map work but it doesn't take that long.
There you have it. Nothing too fancy. Simple always works best for me.