Each modification to the MoO3 executable comes in a '.patch' file. These files are read by the Patcher program to determine their function. They include instructions on how to apply the patch, as well as how to revert back to the original code.
Because the patches are designed to work with the Patcher, it is necessary for them to be located in the same directory as the Patcher itself. The recommended location is in a subdirectory off your main MoO3 directory. So, assuming you used the default MoO3 directory to install, it would be:
C:\Program Files\Infogrames Interactive\Master of Orion 3\Patcher\