Remember, textures are now applied per SubTool in 3.5. You can do all you want in the Texture palette, and nothing will affect your model.
If you’re working with a plane or other 3D object then you’d apply the texture to the model using the Tool>Texture Map menu. In the Alpha palette, select your image to be used for masking, then click Tool>Masking>Mask By Alpha. Now simply press Tool>Visibility>HidePt.
Or if your texture has pure black where you want polys to be hidden, you don’t need to mess with the alpha at all. Just apply your texture to the model and turn on Tool>Texture Map>Transparent.