I'm tinkering with a Super Mutant retexture at the moment and I'm wondering how I go about applying said texture to the creature. Is done through the GECK or through NifSkope?

You have to make a new nif file with all of its BSShaderTexture Sets pointing to you new textures. Then place that nif into the proper creature folder with a new (different) name. Then from a copy of a creature's model list tab, you can select the new nif (with the new textures). That will show the creature with your new textures.

Ok Thanks for the info.

what program would I use to do this, and would I just use the mesh for the creature and make a new copy of it with a different name?

Nifskope is free and is used by just about everybody to retexture things using the NIF method. Nifskope will also let you know all the textures that are applied to an object, and where they can be found in the extracted BSA textures file.

Yes, you take the vanilla NIF and copy it, giving it a new name.

Is there a new version of nifskope out? my version doesn't seem to be able to do this, also the deathclaw model doesn't load in the render screen.
my version is 1.0.15

the latest version is either 1.0.22 or 1.0.23, either will work, its just been a while since ive checked XD