I'm trying to make some custom skins for the cube, and when I open up ALL the texture files, I get the cube, but no aperture science logo, which is what I want to edit. I opened up the companion cube vmt, and find that there's nothing defining the heart replacing the logo. Where is the logo, so I can edit it?

hm.

just checked this out, took the WCC from the portal gcf.
It looked fine to me - I saw the heart on the box right in the center, everything looked normal. Are you sure it was the right VTF (materials/models/props/metal_box_skin001)? Check again; I can't think of any other problems, maybe someone else could be more a help.

Yep.

Are you changing the vtf to a tga? I'm loading the vtf directly with the vtf plugin for Photoshop. It might be broken, though, considering that every image I load is semi-transparent, where it isn't like that in the game.

The vtf plugin has not been updated in a very long time, and is not compatable with the latest (Orange Box) version of the vtf file structure.

Long story short, use vtfedit.