So then provided I want to go through and download and extract everything by hand (which is probably just as well), there should in fact be no reason for me to use the BWS at all. Just get the games installed, patched, get the BG1 missing files, test play it, download and unpack hundreds of mods, and then execute the install.bat.
One more stupid question: When I extract certain mods (usually gibberlings three and such) in to the main folder, the Weidu console pops up and starts to install, at which point I quickly close it out before any files get moved around. That's fine, right? No harm done.
Thanks to all for the swift and informative advice, helping my girlfriend get one step closer to becoming a Baldur's Gate Widow.