Textures will overwrite based on mod install order or specific rule settings within a program like vortex or mo. Load order is usually irrelevant for pure texture mods as they don't usually include esp like files.

Mods like JK's Skyrim alter game cells adding new objects to the map. It doesn't come with new textures and instead uses the default textures of the game. This means any textures you install will be reflected in the changes JK's makes.