A preexisting FMS system may be upgraded to increase its functionality by optimizing the control of autopilot and auto-throttle functions and replacing other preexisting components with different components for enhancing the functionality of the FMS system. The preexisting IRU, CADC, DME receiver and DFGC in the upgraded FMS system are in communication with the legacy AFMC but, instead of employing the legacy EFIS, the EFIS is replaced by a data concentrator unit as well as the display control panel and integrated flat panel display, and a GPS receiver. The upgraded FMS system is capable of iteratively controlling the autopilot and auto-throttle during all phases of flight and of such increased functionality as increased navigation database storage capacity, RNP, VNAV, LPV and RNAV capability utilizing a GPS based navigation solution, and RTA capability, while still enabling the legacy AFMC to exploit its aircraft performance capabilities throughout the flight.