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Greenlea:
hmm... it took me a little while to figure the whole thing out myself (didn't really understand) but I got it eventually. Maybe if I can exlpain it in my own words it will be easier to understand:
1.) Open your mesh file, click "geometric data container", click "plugin view" tab, click "items 3" tab.
2.) Click on your inner-most layer alpha (there should be 2)
(If you using milkshape you can check to see which parts of your mesh belong to which alphas, by going into the groups tab [there's 2 alphas per peice of you mesh]. Click on an alpha and press select. It should apear red on your model. Now just remember that order they're all in)
3.) Change the opacity of "both" innermost alphas to 0x00000001
4.) for the next 2 aphas out, change the opacity to 0x00000002.
5.) for the next 2 out, 0x00000003 and so on.
(Some of the larger numbers are represented differently so check the original thread) I could be wrong on some things too but this is what worked for me.
Hope this will help