First off, version 3.2a was killed, as version 4.0 was released. There is a link in this section, under a post by my name, that will allow you to install Version 4.0. You also do not need to assign any masterbases. When you open the Magic Workstation program, goto "File, Open Libraries" and choose the file "Warcraft.mwbase". This will open up all the WoW cards available for using in decks. I would then recommend switching to "Deck Edit Mode" to build a deck. Thats's it. I have no idea what the assign masterbase function is, but I know I NEVER use it.
Must get ready for Conts... (sounds much worse than Nats... lol) - Northern General