You will need to setup a User Defined Field, Designate the Employee as 1099 and Export the 1099-R Information to the Forms Menu.

User Defined Field
At the A-T-F Payroll Menu:

Select Payer>Payer Edit>User Defined Fields.

Click the Define Field button, from Template select 1099 Payments and click OK.

On the Edit screen

Edit the Field Name, if needed, select 1099-R as the Form, select the Box and click OK.

Designate the Employee as 1099

At the A-T-F Payroll menu,

Click Input, highlight the 1099 employee click Edit and click the Status Information tab.

Select 1099 or Both from W-2 or 1099 drop-down and click OK.

When entering checks make sure to enter the 1099-R amount in the field that was created. 

Export the 1099-R Information to the Forms Menu
At the A-T-F Payroll Menu,

Select Forms>X.Export 1099 Data to Forms Menu and follow the prompts to export the 1099-R data.