I use the large clear pouch in my Imago. I find that if I put it in upside/down, that is with the zipper toward the floor, things are neater on top. In fact, I did that today, and had a folder and a notebook in one pouch to keep my bag tidy for study group.
I am now, when feasible, using solely my Imago and Large cafe Bag for school. I have too much stuff to schlep on Mondays to be contained in the Imago (hence the Zephyr is on my radar), but for the other days, I try to make it so that I can just swap out large clear pouches and the text(s) (as needed) for that class.
I am also using a medium clear pouch as my school supply case, and I keep my pencil case (with pencils) in the medium case too. A little trick I developed is to tape up my pencil sharpener, so the shavings can't escape. They had really dirtied my pencil case, but things are much better now.
I had to expand to using the medium pouch because I also keep a stapler, small tape roll, various pens and highlighters, etc. The pencil case was fine until I added the stapler to my tools. Also, I had the previous problem of the leaky pencil sharpener so until I diagnosed what was doing this I segregated all pencil materials to the pencil case and everything else to the medium pouch (which contained the pencil case.)
OH! A major point in using any of the clear pouches: the urethane side must face fabric. I usually have it face the back of the bag and slide it down. If it were facing my text book and I tried to slide it in it would grip the book and be really tough to slide. Slides like ice on fabric, though.
I will post a couple of pics below. BTW, the bag closes just fine. The pouches are roomier than 8 1/2 by 11. So if they get a bit wrappy-round at the ends the contents in my case are fine.