Hi Danohu
Are you using 6.314 or earlier?
I think the MDL format in those versions cannot handle multiple textures-- so if your 3ds file has a skin for the face and another skin for the eyeballs, it's just going to wrap the first skin around the whole model. You could paint the eyeballs directly on the face in this situation.
The 6.4x beta version will support multiple textures, however, so you could just try working with the new version.
Okay, but here's a question for some experts out there.. why do 6.3 and earlier versions allow you to actually have more than one skin in the MED editor, but it doesn't support multiple textures like 6.40 does? What's the difference? Are those only for mipmaps?