A method is provided for preparing a plurality of systems that include respective programmable integrated circuits (ICs) of the same type. A plurality of circuit designs is partitioned into a base design and respective supplemental designs. The base design includes a set of input/output pins utilized by any of the plurality of circuit designs. A supplemental bitstream is generated for each of the supplemental designs. A first bitstream is generated for implementing the base circuit design, a communication module, and a reconfiguration module in a first portion of programmable resources of the programmable IC. The reconfiguration module is configured to program, in response to each respective one of the supplemental bitstreams received via the communication module, a second portion of the programmable resources with the supplemental bitstream to implement a corresponding one of the plurality of circuit designs.