I see. (a bit misleading that they put that option into the installer when it doesn't work)
AFAIK you can install nearly every mod of worth via BWS. That doesn't always mean they install correctly, however - mod authors have to provide timely info to the BWS maintainers regarding updates or problems creep in. Then you have the simple fact that BWS is handling hundreds of mods, so errors will occur even with the best of intentions and most diligent of efforts.
I was by no means diminishing the effort of the creators of BWS, or all the modders. I am thrilled that there are people putting in the effort to make Baldur's Gate a richer experience. Also, I installed BG1Tutu a few years ago and found that experience to be an absolute nightmare. So I was naturally very pleased when I discovered BWS.
I only wish using BWS was as simple as using a Linux package manager, and that there were clear authoritative sources and instructions instead of it all being scattered on forums across the Web (seemingly).
[...]But long story short..you install EET or any other mega-mod first and then use BWS on it if its possible.
Here I learned something new; I thought BWS was used to create EET. This might be why my attempt at BWS did not produce the desired result. So you're saying that I e.g. follow these instructions: https://cdn.rawgit.c...readme-EET.html to create EET, and then mod it with BWS afterwards. Will BWS correctly identify that the-thing-I-am-modding is EET, and allow me to install both BG1 and BG2 mods?