from the file menu select "Render>Settings..." the "Color" tab will let you change the Highlight color to what ever you want i use yellow because it's easy to see.
once you have a corner selected you can right click on the corner (when the cross turns to and arrow) and select connected then you can move it somewhere that it's alone and also to figure out if you have the correct one.
it's a bit of a pain but what in Modding MW isn't...
Edit: if you have the UV Map window off to the side so you can see the mesh you can see the effect moving the UV around has on it
once you have a corner selected you can right click on the corner (when the cross turns to and arrow) and select connected then you can move it somewhere that it's alone and also to figure out if you have the correct one.
it's a bit of a pain but what in Modding MW isn't...
Edit: if you have the UV Map window off to the side so you can see the mesh you can see the effect moving the UV around has on it
I did that -> http://img98.imageshack.us/img98/1181/34241102.jpg
And the horizontal wooden beam still looks the same in the CS -> http://img714.imageshack.us/img714/6189/14847811.jpg
Are you talking about seeing the affect it (moving the selected part around) has on the NifSkope model or the construction set object?
EDIT: There just has to be a more sophisticated way than doing this blindly in Nifskope. And I sincerely put emphasis on the word "blindly" because the only way to see what I've done is to replace the mesh in my data files and delete and place the object back in the world via the Construction Set. Can Blender actually show you in real time what you're doing to a texture? using the actual textures (not that white stuff we see in NifSkope).