Sorry I didn't get back to you earlier but either it was me or the forums were amazingly and suckily slow or unavailable to me most of the day...
WINE is a wierd one and installs itself all over the place.
The wine.conf file should be in the /etc/wine directory. The install also creates a little "dot" directory in the user's /home diectory, ie., /home/youruser/.wine, where other little files will be written as you run apps with it. The actual executables are in /usr/bin, eg., "wine", "wineserver", etc.
Since in most cases, the path to /usr/bin is global by default, once you edit your config file and go to run a program, you don't have to change to /usr/bin.... you can change to the program's directory and run it from there.
So for example, in my case when I run SETI, I mount the windoze directory where I have the SETI executable, change to my SETI directory, and then run WINE like this:
wine -- winver nt40 -- seti303.exe <parameters>
where I had changed the win CLI executable name to "seti303.exe".
Hope this helps a little?