To "use" the YDC files simply find your profile folder on your computer. If you installed YuGiOh! Online 2 with default settings this folder would be "c:\program files\yu-gi-oh! online 2\profiles\[avatar name]" where avatar name is the name you click after logging on to the game.
Simply place the YDC file in this folder, and you can now choose it in "edit deck" under "load deck". If you have questions feel free to email me and ask.