During undergrad, I'd use both. My laptop was too cumbersome to carry in the messenger bag, so I used my backpack for hauling that back and forth, but I would leave it on campus (we had a locker at the on-campus job I had) and use one of my messenger bags when I was only carrying notebooks and a textbook or two.
Then again, I found that using the messenger bag threw off my balance when I would rollerblade to campus, so that's had me using the backpack more than I otherwise would have.