I am on windows:
After I unzip the new downloaded file, I hold Ctrl and double click both the old version's folder and the new version's folder. Then in the new version's folder, I hold Ctrl and A to select all and then drag all those files within the updated file's folder into the previous version's folder. It will empty the new version folder and move everything to the old version folder. A window will pop up asking whether I want to replace or skip files that are duplicates, choose to replace (all) files when requested. That way all the updated files overwrite the old ones but leave your saves/screenshots/everything you altered safe.
I hope that helps any.