I had some free time and decides to write an small and rather simplistic Mod Manager that as of now only works for the Steam version since i am not sure where GOG does install the game. You can either extract the files your self and but them in there or just put the. If you place an SMAPI update there it will ask you if you want to update SMAPI on launch.
The programm will now create and Folder 'Update' in the dir in which it is residing.