Consider having bunk beds in the room, rather than placing both beds on the floor. This will give you more floor space. You and your roommate will both need to agree to this arrangement and you'll have to agree on who gets the top bunk and who gets the bottom bunk.
Designate two areas for your desks. You and your roommate will each need a separate desk for studying and completing school assignments. This bit of space will be small, but just having it separate from your roommate will help establish a sense of personal space.
Add a comfortable chair in front of the desk. Make sure the height of the chair works well with the desk. This chair can double as your computer chair and a lounging chair for when you're hanging out or when you have visitors.
Put in a mini-refrigerator. If possible, add a small shelf next to the refrigerator. This will serve as the kitchen area. Try to put the kitchen area closer to the desks than the beds.
Move in a few dressers if you have space. You might only have space for one large dresser. If this is the case, you and your roommate should each choose drawers. Label the drawers and put the dresser in an area where you can get dressed privately, even if your roommate opens the dorm room door. Hang a full length mirror on the door or a nearby wall to complete the dressing area.