Congratulations! You have organized areas of your room that are for you. Now we are going to switch our focus to organization for your students. Each of my groups has a white magazine file box (I call them "Cubbies"). Each student has a numbered folder (all the same color - I used yellow at one building and green at another - yellow and green are my districts colors). I know many teachers are against numbering their students because it diminishes them to a number instead of a person BUT I'm not going to create new folders every year. The only time my students need to use their number is when looking for their folder in their "cubbie". All the students papers go in their folder and books go in the magazine file "cubbie". That group and substitutes can easily see where that groups materials are.
I got my magazine files at Ikea but you can find them online or get them for free from Wal-mart and Target. During back to school sales, big stores use magazine files to hold the folders and notebooks. Go and consolidate their notebooks/folders and load your cart with the empty boxes. Ask if you can take them - they always say yes because they just throw them away.
You could also use mailboxes (like classroom teachers have) and each student gets their own slot. I have seen classroom teachers keep students work in filing crates around the room so when she needs them to get their reading notebooks, the class disperses throughout the room. You could use baskets or bins for each group. Look at the layout of your room and look for containers that you like. Let that determine what you use. You want your room to be visually pleasing so try to stick to the same type of container for every group.