Always open up your material browser and click the little button that says standard. Look around a bit, you'll find it. A new window will pop up. Look for multi/sub-object. Click it.
You can now separate your materials by ID. Good, right? Not unless the faces on your BSP have IDs applied to them as well.
Convert your model to editable mesh, this is easy. Just right click on the model and highlight convert. Click editable mesh from the dropdown. Select whatever faces you want to change and scroll all the way down to "Skin". You can see where to change material IDs. Either use the arrows or enter the ID number to apply specific textures to your map.
Too confusing?
http://hce.halomaps.org/hek/