Amounts received by an employee under a written educational assistance plan are excluded from taxable income, up to $5,250 per year. It would appear that your employer has the intention to treat the payment you just received as a 2016 benefit and the payment in May as your 2017 benefit, both within the maximum for the respective year.
The amount received should not be included in Box 1 of Form W-2. Since the benefit is not taxed, you have no reporting obligation on your tax return.
For more information, please see IRS Pub. 970 Tax Benefits for Education.