Just replace the dosbox.exe in a GOG game folder with this one. Also make sure to set in the DOSBox config file for every game these parameters:
fullresolution=desktop
output=openglnb
aspect=false
scaler=normal3x
autofit=false
Note that you shouldn't copy the config file provided with DOSBox CRT, as every DOS game on GOG comes with its own optimized config file. You just need to change some of the lines.