Yes, the program will automatically fill in Line 9 for AEIC on the 941, providing you have everything set up correctly.

• First, you will have to add a User Defined Field for the AEIC. To do this go to Payer>Payer Edit>User Defined Fields, double-click on the first <blank> line and the select Examples.  Highlight Advanced EIC Payments and click Select.  Select Apply and then OK.
• Once that is completed, close the Payer Edit and click on Input.  When you enter an employee's check, please make sure to enter the AEIC amount in the correct field (AEIC). 
• If you want the program to calculate the AEIC then you must also, select the employee receiving the AEIC payment and click Edit. Select Live Payroll Parameters and enter the  AEIC table number choose either A or B depending on which the employee needs.  Please refer to the IRS documentation for more information regarding the AEIC table numbers.