I don't know if you have done so already, but before you can play WoW on MWS you need to go to
http://mws.infogathering.com and download and run the Version 7.0 FULL INSTALL. This will give you all the cards you can use for WoW to date (tournament legal cards only). After running the install, go into Magic Workstation and goto "File, Open Libraries". Browse to this location (c:\program files\magic workstation) and select the file called "Warcraft.mwbase". Now you can start building a deck by going to "File, New Deck". I would suggest switching the view to the Deck Edit Mode (Under View, Deck Edit Mode or hit ctrl + F2). After you build your deck, putting the hero card in the Sideboard, open the MWSPlay program. Hit F2. In this window, give yourself a name, set your starting life to 0, starting hand size to 7, and load the deck you made in the other program. When done, click on start game. In the next window, click the button called "Call". This will call up the server in the dropdown above (default should be mwsplay.net). Now just join a game that has a WoW or Warcraft description, or create your own game and wait for a player. If you make your own, it's a good idea to put WOW in the description and since you are new to MWS, you might want to add that as well. Most players are nice, but some will quit outright and be rude if they find themselves playing someone who doesn't know MWS. I cannot play at work, so i can't help you with the game mechanics right now, but I'm sure one of the nice players from this thread will help you out!