like what i want to do is get new skeletons for every NPC so they can bend their legs when they walk (their movement is horrible .-.) then get more updated looking graphics over characters and then retexture the world with skyrim textures

vanilla looks too clunky .-. and NPC's move really clunky i swear their legs dont bend or anything

By "how to mod" do you mean make mods yourself or install them? It's not clear if what you describe are your planned endeavours in the Construction Set / 3DS Max / Photoshop or what you are wondering already exist.

If the former: good luck! If the latter: get MGSO

There are a couple animation replacers out there, see first post http://www.gamesas.com/topic/1071872-animation-mod-list/. If you mean you wish to make new ones, that will require either 3dsmax or Blender.