Income and expenses paid to me reported as one lump sum on 1099?

The company I contract for gives me one check, which includes the per diem rate and also the expenses I accrued doing the job, mileage (they pay only $.44 per mile), motel room (I travel to places for many months at a time. Therefore, when I look at the 1099 it includes the expenses also. What amount do I put on my taxes as income...I don't want to have to pay taxes on reimbursement amounts. How does the IRS know that part of the income listed on the 1099 is for reimbursement?