For the purpose you want, you actually do not need to copy the files over. you can run WOW from within the windows partition. What you really have to do is the following to have everything working as it should:

1. Install the PPA for WINE. You HAVE TO install the PPA which is much better. More info here: How to update Wine to the latest version?




2. Install using winetricks (After having installed Wine) all DirectX 9 components. Since the release of Wine 1.4, you can just install the DirectX that comes with any Windows CD/DVD (eg: The DirectX 10 that comes with Skyrim). That should be enough to get DirectX working.




3. Install the latest drivers for Intel, Nvidia or Ati. All of which you can find/install with this PPA: How do I install the latest Nvidia drivers via the Additional Drivers tool?




4. Follow this link with any additional relevant information about WoW: http://appdb.winehq.org/objectManager.php?sClass=version&iId=25610




5. Create a desktop shortcut/launcher as mentioned in this question to have a working one click icon: How can I edit/create new launcher items in Unity by hand? (Easy way here: https://askubuntu.com/a/128284/7035 )




6. Edit the Desktop shortcut and in the command line type: wine "DIR" -opengl where DIR is the complete location of your Wow.exe file. For example in my case wine "/media/fun/games/World of Warcraft/Wow.exe" -opengl". The OpenGL is to give you more available graphics options. You can also remove it but for most video cards it is better to have it there to make the game run smoother.

If you still want to copy the Wow folder, you can put it on your Ubuntu home folder and do the same steps mentioned before. Just wanted to point out that you can run the game from the same Windows partition, does saving you space and time.