I think this is the info you need. If you're in the Finder and traversing one of the directory paths below, and you run into what looks like a file but the directory path indicates it should be a directory, just right-click (or control-click) on it and choose Show Package Contents, then continue traversing the path.
Kyrub's patch files should overwrite the files here:
/Applications/Master of Orion 1.app/Contents/Resources/game/Master Of Orion.app/Contents/Resources/Master Of Orion.boxer/C.harddisk
For the save games, with the Finder as the currently active application, hold down the option key and at the top of the screen choose the menu item Go->Library. The save games are here:
~/Library/Application Support/Boxer/Gamebox States/com.gog.master-of-orion/Current.boxerstate/C.harddisk
Kyrub's patch files should overwrite the files here:
/Applications/Master of Orion 1.app/Contents/Resources/game/Master Of Orion.app/Contents/Resources/Master Of Orion.boxer/C.harddisk
For the save games, with the Finder as the currently active application, hold down the option key and at the top of the screen choose the menu item Go->Library. The save games are here:
~/Library/Application Support/Boxer/Gamebox States/com.gog.master-of-orion/Current.boxerstate/C.harddisk