You can't make AmiDock transparent on OS3.x, only in the OS4 version. You can, however, do what I did and take a slice of your wallpaper where your dock would be, then use that as the texture of the dock. This would give the effect of the dock being transparent. You would still get a border round the dock though.
If you want a totally transparent dock, you may need to look for a different programme.
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moto