The agency is the top level of commissions. Advisors Assistant will track commissions for multiple agencies, but that feature is optional at an additional cost. When you are tracking for one agency, it has the same name as the licensee of the Advisors Assistant system.
Typically, the company pays the agency and the agency pays producers and managers. However, producers and managers can be paid directly by the company. These settings are set in the Rate Tables.
Additional agencies may be tracked for an additional licence fee.