Well, not too familiar. I have gotten it to the point where I can run small stuff like winzip, but for example Monkey Island 4 still has trouble recognizing the CD's.
Make sure you have your windows partition mounted when you run tools/wineinstall from the source tree. If it really fails to find windows, the config file is in .wine/config, but I wouldn't know how to find out which registry entries to add. That's where the wineinstall script is for.