first, I'd put the bed (twin I hope!) up against a wall.
second, I wonder if a table top on top of two file cabinets would allow you to store paper, etc in the file cabinets and use up the space under your work table. even a rolling cart with files for cardstock that you store under the table would work.
finally, whatever system you use (shelves, bookcases, rolling carts) will work much better if you label every drawer, basket, etc.