I downloaded the update ygopro. I installed it but when i opened it it opened up a new Ygopro. I don't know how to extract the update file to the Ygopro Folder. How can I extract it to my Ygopro Folder?
If you are updating the game manually you need to move the .rar file into your YgoPro folder, then you can extract it inside that folder overwriting the older files with the new ones.

If you are updating the game automatically you just need to run the game and it will install it for you.

And you can always just download the full version and move decks and other things across to the new version.