Hi and welcome
Most games are always release new versions that contain all previous content, so download the new(updated) Version and unpack it to your desired location. delete the previous Version. NEVER put the updated game into the old game folder, that messes up everything.
Patches: (i don't know of a dev who releases patches for new updates instead of the "full" version, but i cannot know every game xD) are single files that can be put into the game folder.
Save FIles:
Ren'Py games save their files at two locations (in the game folder itself and on your SystemHDD (user/username/appdata/roaming or locallow or local
RPGM saves are in the game folder, you'll need to back up them before deleting the game
Unity saves are although into the systemHDD (user/etc/etc) search for the name of the game in the three folders (roaming, local, locallow)