As a contribution to the research into HCCI engines which have a potential of achieving low fuel consumption with low particulate and low NOx emissions, a six zone simulation model coupled with the cycle simulation code AVL Boost was previously developed. The model uses comprehensive chemical kinetics and shows good agreement with experimental results. At the point of transition from the gas exchange process to the high pressure cycle, which is multi-zonal, the model assumes equal gas mixtures in all zones. Therefore, the model is suitable for perfectly homogeneous mixtures, and since it has no ability to receive fuel during compression, the mixture has to be prepared outside the cylinder. Further development of this model, which will be shown in this paper, includes the introduction of initial conditions with non-uniform mixtures and the possibility of receiving fuel during compression. This means that at the intake valve closure, the model will be able to calculate different mass fractions of species in different zones. Non-uniform gas mixtures will be defined by input parameters from the user of the calculation. These parameters can be obtained with more detailed CFD calculations of the gas exchange process. Also, a possibility of introducing fuel during the compression stroke will allow the user to simulate engines with direct injection of fuel. Besides the description of a physical and a mathematical model, which is used for the expansion of model possibilities, and besides validation results of the perfectly homogeneous engine, some results of calculations with non-uniform mixtures and fuel injection are shown. Based on the analysis of these results, conclusions regarding the achieved improvement are drawn.