What a mess. You don't need to deduct your expenses, you got some reimbursements tax free and some taxed. If you want to try and deduct your expenses, enter all your work expenses (that you can prove with mileage records, receipts etc.) and then when you are asked about non-taxed reimbursements, enter that amount which will be subtracted from the deduction. You will end up with whatever remaining amount is legally deductible.
