The Swift X-ray Telescope (XRT) is a CCD based X-ray telescope designed for localization, spectroscopy and long term light curve monitoring of Gamma-Ray Bursts and their X-ray afterglows. Since the launch of Swift in November 2004, the XRT has undergone significant evolution in the way it is operated. Shortly after launch there was a failure of the CCD thermo-electric cooling system, which led to the XRT team being required to devise a method of keeping the CCD temperature below -50C utilizing only passive cooling by minimizing the exposure of the XRT radiator to the Earth. We present in this paper an update on how the modeling of this passive cooling method has improved in first -1000 days since the method was devised, and the success rate of this method in day-to-day planning. We also discuss the changes to the operational modes and onboard software of the XRT. These changes include improved rapid data product generation in order to improve speed of rapid Gamma-Ray Burst response and localization to the community; changes to the way XRT observation modes are chosen in order to better fine tune data acquisition to a particular science goal; reduction of "mode switching" caused by the contamination of the CCD by Earth light or high temperature effects.