FYI, always download the repository version of BWS before you use it. Get it at: https://bitbucket.or...setup/downloads
The mandatory selections that you can't undo are there for good reason. The program will download those and install them as part of the Installation process. The installpack and fixpack fix several bugs fixed nowhere else that are introduced by mods. As such, BWP/BWS helps ensure the most bugfree game as possible. If you were doing, the BWP instead, you'd also have to download all of these, BWS just makes this easier for you to auto download and auto install.
What's in your download folder and what your BG2 instance installs are 2 different things. BWS will check your download folder for every mod that you had checked to be part of your install. If the mod is in the folder, BWS will check the next mod. If a mod is not in the folder, BWS will auto download that mod into the folder
Once BWS verifies that you have every mod you need fully downloaded then it will prompt you to install your "instance" which is only the list of mods that you had checked earlier. BWS will not install mods that were not checked. Mods in the Downloads folder that weren't selected will not be part of the install that BWS does.
I hope that's clear,
Bill