...Erm. Which better armor textures do you mean? Darknut's?
First of all, if you're replacing the vanilla textures there's no overwriting anything--all the game's vanilla textures are stored in the BSA files. Second, if it is Darknut's mod you're installing, IIRC he has all the armors in separate folders (for Nordic, Steel, etc.). You have to copy all the textures
out of those folders and into the main Data File\Textures folder. No sub-folders.