I suppose you ask all the BWS questions in the BWS thread I referenced above. I do not know about current BWS, last used it like 2 years ago for BGT...
Then assuming I try to be "badass" and go with the manual install after all should I install Sandrah first or last if I go with only the required mods for her?
Are you sure?
Because you need a clean install of BGEE (+ modmerge, if you have a steam or gog game) and a clean BG2EE.
Then you need to install the BG1 mods you want into BGEE
Then you run EET core in the BG2EE
Then you install the BG2 contents mods in BG2EE and prior to installing the ones that need fixes, you do the fixes on them
Then you install Sandrah
Then you install the fixed for EET BP-BGT Worldmap
Then you install tweak mods if you like
Then you run EET_end
Then you do GUI mods if you want
Then you pray that it all works...