Is your GI Bill going directly to the school or to you? Which version of the GI Bill do you fall under? The reserve GI Bill check I used in college almost 20 years ago went directly to me every month. The GI Bill I paid into after entering active duty, and the new Post-911 GI Bill (which for me are now one in the same, and which those serving now get without having to pay into) are paid as a stipend directly to the veteran with the amount dependant on your course load. Bottom line is the GI Bill is not meant to pay solely for tuition, but to compensate veterans seeking higher education. The newest version is even transferrable to family members (my 2 kids can essentially get 2 years of school each paid for by the new GI Bill).
I also received a small $700 scholarship for each of the first 2 years I was in college. My folks, however, paid my tuition in full at the start of each semester, so the scholarship checks, which were sent to the university, created a credit balance in my account. Because of this, the university cut me a check each year for the overage. I also received my GI Bill on top of this, all of which went towards food, gas, etc.
I'd defineately fo with the earlier recommendation of seeing the VA rep at your school, I know mine helped me out a lot the first year when I was learning the system.