A method and apparatus for generating user clocks in a prototyping system is disclosed. A prototyping system has a plurality of programmable logic chips that are each programmed with one or more partition of a prototyped circuit design. For a circuit design having multiple user clock signals, each partition uses some or all of the user clocks. A reference clock signal is externally generated, and received by each of the programmable logic chips. Using a phase-locked loop, a plurality of in-phase higher frequency clock signals are generated from the reference clock signal. The user clock signals are then generated from these higher frequency signals using a plurality of divider circuits. Reset circuitry implemented in one of the programmable logic chips transmits a common reset signal to the divider circuits, maintaining the phase relationship of each user clock across the programmable logic chips.