I can't render an Uncompressed Alpha layer. Help

HI
I did my project in premiere. One layer has the band playing and the layer above has all the cut away scenes.
I exported the bottom layer of the band footage and did all the colour correction etc on it and am now trying to do the same for the second layer.
The problem is there are gaps in the footage where the layer below would be playing. So when I export the second layer, black is displayed and this covers up the footage below in After Effects. A uncompressed 10bit AVI does not give me an option of millions+ colours or rendering with alpha. I just tried rendering as un uncompressed Quicktime codec with millions + colours ticked but it did the same.
How can I get uncompressed footage with an alpha layer so that I can see the footage in the layer below when there is nothing to be displayed in the layer above?
The shoots are different so thats why I'm doing 2 different colour corrections
thanks
Jamie

Using Premiere Pro CS3,
I put a quicktime movie (.mov) I had made in AE with an alpha channel on the timeline.  I just wanted to test to see if I could export out of Premiere as a quicktime movie with an alpha channel.
However, using Export - Movie - under File type, I don't have quicktime as an option.  I do have cineform, but I'm using a regular NTSC widescreen preset.
Has quicktime been added as an option for an output file type say in CS4?
Thanks,
John Rich

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