A controller for a system having at least one variable-capacity, pulse-width modulated compressor and at least one fixed-capacity compressor is provided. The controller may include processing circuitry that modulates the at least one variable-capacity, pulse-width modulated compressor to any capacity substantially between ten percent capacity and one hundred percent capacity. The processing circuitry may determine a desired capacity of the at least one variable capacity, pulse-width modulated compressor based on a load sensor signal and a current run percentage of the at least one variable capacity, pulse-width modulated compressor and may toggle the at least one fixed-capacity compressor between a run mode and a shutdown mode based on the desired capacity of the at least one variable-capacity, pulse-width modulated compressor.