After you have setup your agencies and pay plans you can now assign pay plans to your agencies. Assigning a pay plan to an agency will determine what you pay this agency on a regular basis, allowing you to assign Rep IDs to this agency and RPM will calculate the pay plan rate. 

Top menu >> Agencies  >> Click pay plan name in the Pay plan column

Click Edit

The Pay plan to the left of the edit button will turn into a dropdown. Choose the pay plan you would like to assign and then click OK.