How to mod GOG-Version of BG?

I just bought the GOG-Version of BG which seems to be the Windows-version with a wineskin-Wrapper. I tried to install a mod as described in the Hitchikers Guide, but when I start the setup I get the error message "Please run this program in your Infinity Engine game directory." So there seems to be a problem with the right directory. I think this has to do with the fact, that in the GOG-Wineskin-version the game files are in a virtual "C"-directory and not in the "resources" directory. But perhaps I'm wrong here.
(note: the right waidu version is installed)

Has anyone found a solution to this problem?