A customizable electronic bill payment and presentment system whereby the base logic for software agents need not be changed in order to provide customization to different billers. Rather, customization features are stored in data repositories, preferably in XML format. An administrator can select which agents to activate based upon a customized list of available agents. Then the customized parameters for activating and running the jobs with the agent is further loaded from customized repository files at the appropriate time. Accordingly, customization for a particular biller is achieved by changing data stored in a repository, rather than reprogramming core logic.