A homogeneous charge compression ignition engine is set up by first identifying combinations of compression ratio and exhaust gas percentages for each speed and load across the engines operating range. These identified ratios and exhaust gas percentages can then be converted into geometric compression ratio controller settings and exhaust gas recirculation rate controller settings that are mapped against speed and load, and made available to the electronic engine controller. This provides the engine controller with a look up table of what compression ratio and exhaust gas rates should be at each speed and load. The engine controller also balances at least one of combustion phasing and energy release among a plurality of cylinders in order to enable higher load operation.