BOSS sorts them, NMM makes it easy to download and track the mods you have by their archive. You can install with NMM, but I always use WB/BAIN to install them, because apparently it does a better job of cleanly uninstalling, although you'd have to ask somebody exactly how, because I can't remember. Also, WB is necessary when you have multiple mods altering the same leveled lists, among other things,
For example., if you download two different weapons mods that add new weapons to the game and add them to various bandits and whatnot around Skyrim, they are editing the same leveled item list. If you don't use WB, then only the last one loaded will have its effects take place. If you use WB to create a bashed patch, however, it will take their changes and merge them together into one edit of that leveled item list, and you'll see the effects of both take place.
So yeah, get and use NMM, BOSS and WB, as well as SKSE. It sounds daunting but it really isn't that complicated once you do it.