A tool is described to aid in the design and verification of multi-input, multi-output power supply systems. The designer describes the system requirements and constraints to the tool, which allows an iterative exploration of various alternative designs that satisfy the requirements and constraints. Alternative designs may comprise different power supply topologies, multiple controllers or multi-controllers, or configurable controllers that implement the power supply system. The tool generates a design for a power supply system that is reconfigurable to allow for performance optimization. The power supply system is configurable automatically according to a digital control signal. The digital control signal comprises configuration data which establishes the structure of the power supply system, and which determines the output power conditions of the power source. The different conditions generated by configuration data comprise output voltage, sequencing information, current, topology, and other operational conditions such as overload protection.