The first payroll on 1/6/17 is for the two weeks ending 12/31/16. However I cannot enter a pay schedule with this information because FE doesn't recognize when a pay period end date is in a prior year. This will be the same situation for the next several years. All payroll data (W2s, etc.) are for the pay dates not pay period end dates so i do not understand why FE cannot handle this. Please fix this.
If configured properly your 2016 pay schedule should have the period ending 12/31/16 defined. You can easily run a payroll dated 1/6/17 for the period ending 12/31/16.
If your 2016 schedule was not properly set up that way, the system will not allow you to edit it if it has been used on past payroll calculations.
The work around is to create a new EOY pay schedule with one period in it ending 12/31/16. You will have to assign this pay schedule to all the employees, calculate your payroll, then change everyone's pay schedule back to their normal for 2017.
Make sure your 2017 pay schedule is set up properly so this will not be an issue next year.