We used 4 1.5 inch Binders. The one on the left is for Science. We started by putting 50 sheet protectors in it. It's for storing the notebooking page, the answered questions, and science lab forms. The middle binder in the back is the general binder for Preparing. In it we have dividers for grammar, math, and writing which includes the poetry assignments and any other writing, and a miscellaneous tab. My ds has decided to put his written narrations in the writing section , but my dd wanted another divider for it so she has 5 dividers and ds has 4.
The last binder on the back row is the history binder. All of the independent history goes in this one as well as any of the history projects that fit. We started with 50 page protectors in here also. So far we haven't used any dividers in the science or history binders. As the year progresses we may find we need some dividers. On the bottom row left is a composition book for dictation. We are just continuing using our one from last year since it still had room. In the middle is the binder for DITHR. I decided to take apart the student guide and just put it in a binder so that we only have the units that we are going to do this year. On the right is the Common Place Book. I found these leather look journals at Dollar General. I gave my dc the choice of whether to use the journal or a regular composition notebook and they chose the journal. I thought they might choose the composition book since the lines are larger and there is more room for writing, but they like the special journal.
On the very bottom is the vocabulary file. We use the larger index cards and this inexpensive holder that I got at Target. Here is how we set-up the rest of our books. Each dc has a soft file basket for their notebooks and vocabulary holder. All of their other notebooks are in the magazine holder next to their basket. The clear magazine holder in the center holds the independent history and science books that they are using for their current unit. It seemed like a good idea to have a central place so that one dc would be able know if the book was in use currently.
All of the rest of our books for Preparing are on this one shelf. I rotate out the ones that they need each week for their independent activities.
I also tabbed our guide with those neat sticky tabs this year. I have a marker for our current unit, dictation, and poetry. I have a fourth one in there for the unit that I'm currently reading myself.
I'm finding those sticky tabs really useful!
So that is what we are using and how we are set-up for this year. So far it is working great!
Yeah, I know, flying by the seat of my pants, but I knew I had this post in my back pocket. 
Could you enlighten me?