you can just overwrite all files. Keep in mind that if you use additional mods, you must manually merge them.
Continuing a savegame is possible, but you will not get any of the new scenario fixes until you start a new game.
If you also use the addon, continuing an old save may lead to some weird effects in inheritance laws all over the map: any country with the monastic supremacy religious law will get the female inheritance law since I had to reuse the tag. Outside of that, there should be no problems.