your employer is doing it all wrong. under an accountable plan where you submit periodic expense reports to detail those expenses and the employer reimburses you, no 1099 is issued to you. the employer takes the deduction for the reimbursement. for you and the employer a benefit not subject to FICA or medicare taxes. the 1099 way you report the income on schedule C and take a deduction for those expenses.
so you net out to zero.
