Im trying to install the 1.5.9 patch, however it can't find the directory for the game from GoG. I thought id just put it in myself, however I can't find the directory for the life of me. I've searched everywhere for an answer, but all I can find is people looking for and finding save files, not the whole directory.

Depends were you installed it too.

If you can't find it: (all assuming Windows)

Re-run the installer, it will tell you were you installed it too.
typing master of orion in the search for WIn8 (maybe 7 as well) onwards, it shall show you Master of orion 2 , hoover over it, right click, properties, open target directory.
In your start menu you shall have an entry for it, same procedure as above.

My steam folder sits in 'program files (x86)'
I am guessing thats the default location. Found my steam game in subfolder:
program files (x86)\steam\steamapps\common\

sorry, I Shoulda been specific. Im on Mac OS Sierra. (yes, I know Mac is shite for games, its what I had available though.)

Shame on you ;) (for not saying directly)

man.....that isn't easy to answer....

>if< you do have a shortcut somewhere you could check even under mac the properties to see where it is installed. But still fun trying to find it I only say / and \ :D

How do you start MoO2? maybe we can go down this route and try to find it ;)

It's not that hard (if you own it on GOG). It helps to know how Macs handle App bundles and that GOG uses Boxer Standalone for all Mac DOS builds. E.G. download the DMG, with 7-zip extract the .hfs file itself from the DMG (4.hfs), then extract all files from the .hfs, and profit. It does depend on where you installed it. Go find the Master Of Orion 2.app, the .app is hidden by default. Right-click - Show Package Contents (or cd into via terminal). Browse to Contents/Resources/game/Master Of Orion 2.app/Contents/Resources/Master Of Orion 2.boxer/C.harddisk. You will need to Show Package Contents on the inner App and possibly the .boxer.
You can edit the MULTI.BAT to run the patch or the Game Info.plist is the Master Of Orion 2.boxer directory.

Great answer!
but you might want to remove my post-link on your second part, otherwise the OP (me thinks) will not get notification that you did provide an answer ;)

Yeah, somebody always has to be a but :D