We present a comprehensive analysis of different techniques available for the spectroscopic analysis of FGK stars and provide a recommended methodology which efficiently estimates accurate stellar atmospheric parameters for large samples of stars. Our analysis includes a simultaneous equivalent width analysis of FeI and FeII spectral lines, and for the first time, utilizes on-the-fly non-local thermodynamic equilibrium (NLTE) corrections of individual FeI lines. We further investigate several temperature scales, finding that estimates from Balmer line measurements provide the most accurate effective temperatures at all metallicities. We apply our analysis to a large sample of both dwarf and giant stars selected from the Radial Velocity Experiment (RAVE) survey. We then show that the difference between parameters determined by our method and that by the standard 1D LTE excitation-ionization balance of Fe reveals substantial systematic biases: up to 400K in effective temperature, 1.0dex in surface gravity and 0.4dex in metallicity for stars with [Fe/H]~-2.5. This has large implications for the study of the stellar populations in the Milky Way.