Gwenny,
Great idea to review what worked. And is so exciting getting ready to start next year. My dd is on until 25 now but we are going to go through June to finish and start back up in August with CTC.
For us, we use a 3" binder for my dd's history, science and poetry/writing. We used one student notebook for each of these subjects: vocabulary, spelling, grammar and common place book. We did not use page protectors though because then the book gets way to thick. And you didn't do anything wrong, the page protectors do stick out so then you can't see the tabs. We did not hesitate to punch holes in everything and then slap them right into the binder.
I also did cut the spine off of my teacher's manual and put it into a 3 ring binder as well. I found that I could reorder the pages as I wanted to be. So my first tab was the current week. This way I could show my dd everything she had to do for the week and she could easily find where she was in the book. I also highlighted (yes I marked the guide) everything that "I" in pink and everything that had a "T". And then I wrote in each box the number of minutes I thought each would take her to do. Even with 3 kids, this is great because I would do the same thing for everyone else. Once my dd finished it, she would pencil a checkmark. At the end of the unit, I could go back in and erase the check marks. I think put the poetry in the next tab. I put the spelling next. And then math in the next tab. Then I had the rest of the weeks of work in the next tabs. And then anything else I didn't pull forward I kept at the end. For me, this was a great fit because I kept everything close to the front of the binder that I was using regularly. I really liked that.
Also - this year my dd had her own desk. I don't know if others have the space for that but it was great! We kept her notebooks and stuff in plastic rectangular bin on the table. Then I had book ends where her TM (in the 2" binder) was on the out side of one end and her student binder (3" binder) on the outside on the other end. In between the two with the bookends we had all the books she was reading by herself at that time. Then we had a desk organizer to hold papers in a file folder for her that she could pick from for her writing activities.
Next year though, I want to acquire 1 more table for my home for my kids to use for school. But I would like the kids spaces to be a little bit more portable. So that no one has a specific "desk" and that they can around move and work anywhere they need to. So I am looking at getting each child a desk organizer like this:
http://www.staples.com/Staples-The-Desk ... ze=certona. This way I can put all of their books that they are using in here and their student notebooks. It won't hold their binders though but I think that will be fine. And then it will also hold their pencils and supplies as well. This would make their space a lot more portable. So I don't know. I am still praying about it though.
We like to use a big 3-ring binder with tabbed sections for much of our dc's work too. 
HTH as you have fun setting up your organization methods for the year 
My next one about to start needs a lot of help in that area.