You have to download it for every update (those that bought it from Steam can have the program download the patch to the newest public version automatically). As long as you have the extracted files replace the old ones, your save files will carry over to the new version of the game.
You don't even need to do this, you can unpack the new version into a completely separate folder and it will still find your saves because where the inbuilt saves are is completely independent of the folder that the game is located within. You might need to point the game at the folder where you've chosen to keep your local saves (assuming you don't keep them in the same folder as the game) but that's it.