I'm having a few issues with Textures not appearing as they should. I am using the atronach base to create other creatures, and the texture issues are slowing that. In-Game and construction set my creature appears to be very shiny, like made out of glass. This blocks makes the creature unreconizable, as the stone looks more like grey glass. My second is that transparency never shows up. Any advice on this?

I'm very much a beginner at this but it sounds like you are using the wrong compression type. http://www.fsdeveloper.com/wiki/index.php?title=DXT_compression_explained an explanation of the different types. I just googled, you may find something better.

To fix the glossiness issue, open the nif in NifSkope, click on the NiMaterialProperty line(s), and change Specular to 0,0,0 and Diffuse and Ambient to 1,1,1. That should force the game to render the textures just as they appear in the DDS files.

To make your creature partially transparent, take the main texture and add an alpha channel to it. White = no transparency, Black = full transparency (i.e., completely invisible). So a nice shade of gray would work best.
Once that is done, open the NIF you want to display the transparent texture on, find the block for your texture (i.e., the part you want transparent), Right Click>Node>Attach property>NiAlphaProperty. If you then add your texture you should see the mesh/mesh part is transparent.

That's how I made http://tesalliance.org/forums/uploads/1298372582/gallery_775_71_731010.jpg

The creature still appears to be a bit shiny. I'm using the CpRockMoss01 texture of the Frost Atronach if that means anything.

the frost atro probably has a environment map shader enabled. change the nimaterialproperty name to something other than ENVmap2 and texture apply mode from apply_highlight to modulate

also while I am here, other common things to look out for when it comes to mat and tex in oblivion, shininess can be because you either no specular map or a very bright one. Or perhaps the gloss material property is set to 0, this will cause light to beam off the surface in a similar way as if the spec was very bright. set it to 10 at least, if your material is glossier, like plastic, then you can up it as much as you need.10 is the lowest you ever see in Ob and F3.

You can basically ignore the other material properties besides emissive and alpha, I have the impression: spec is overiden if a spec map is present, diffiuse and ambient are overiden if a diffuse map is present and are basically similar to what vert colors, except the material setting is a global slider. a simple test would be to set up an editor marker, 1 with vert color and 1 with the diffuse material, both set to the same color and see how they look in comparison

make sure to test in game itself. nifskope is not representative of the gamebryo renderer in anyway.