If I paid out of pocket for some classes, do I still put the GI Bill amount I got under Veteran Benefits since the GI Bill didn't actually cover the out of pocket cost?

Yes, you must reduce your education expenses by the GI Bill you recieved, but if you also paid for tuition, fees, books and/or supplies out-of-pocket, be sure to also enter those additional expenses. 

After you enter your 1098-T continue through the education section and interviews to also enter the costs of books and supplies. 

If you paid for some of the classes, Box 1 on your 1098-T should be larger than Box 5. 

Compare your school account statement for 2018 with your 1098-T. If the 1098-T doesn't seem right, contact your school's financial aid office.