From my knowledge (and a hell of a lot of pain and frustration) whatever you apply in UED as the third texture is kept as is if it is found in the .UPL. you cannot DEFINE it in the .UPL however. So you can't simply make it change textures by changing where the texture is found in the .UPL. I hope this changes in UT2004.
The third texture, by the way, is set by map channels/groups in whatever 3D program you use.