Understand that transportation expenses for a W-2 employee are no longer deductible by that employee. So your S-Corp would need to have an "accountable plan" to reimburse you with. That's basically where the employee submits receipts and/or mileage logs to the business for expenses incurred in the process of that employee working for the business. THen the business will reimburse that employee for what that employee has provided "in writing" (receipts) to the business, and the business can then deduct the cost. With an "accountable plan" reimbursed expenses are not included in the employee's W-2 earnings and therefore not included in box 1 of the W-2 issued to that employee.
Understand that what the business can deduct is still subject to the "per mile" rate for that business in this case. For 2018, that rate is 54.5 cents per mile. So in addition to gas receipts, the employee will also need to provide the business a mileage log of actual miles driven in the performance of their employment responsibilities. Then the business should only reimburse the employee for actual miles driven in the performance of their job, regardless of what any gas receipts may show.
