On the 941 Aatrix report or State or Federal Tax Report, place your cursor in the employee count field and manually add the number.

The State and Federal Tax reports calculate the number of employees based on the 12th of each month.  This is noted on the form itself. 
For example, if you calculate monthly payroll for 100 employees and enter the period end dates 01/30/14 to 01/30/14 when creating the calculation, none of your employees started, crossed, or ended on the period of the 12th of January.  If  you entered the calculations dates as from period end date 01/01/14 to 01/30/14, all 100 employees would show on the report as 01/12/14 falls within this range.

In short, two items must be true for the reports to take calculations into account to create the employee totals:

1.  The calculation date range must include the 12th of the month
2.  The pay date needs to fall within the reporting period for the report (so if it’s a quarterly report, it would have to be in that quarter)

For more information on the 941 report, review How to reconcile the 941 Tax Report