I don't know, I find working with Alpha channel in Photoshp very easy. Either just don't use a background, but work over transparency or, if you prefer some coloured background for visibility, have it in it's own layer at the bottom and delete it before you save/flatten.
That way you can just save the transparency as alpha. No hassle at all. Don't know about other applications, but I'd guess they handle it similarily.
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