Ok I am starting skyrim from scratch and question is should I or is it required to extract all the skyrim bsa files into the data directory or should they be left alone and continue with the game?

Contiue with the game with some mods I meant at the end

You don't really need to extract the official bsa's unless you plan on using the files inside for a mod. Plus if you're using a lot of mods, then I would suggest against it if only to keep your folders clean if you plan to uninstall or install anything new.