How to go about using alphas?

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Well, what you wanna do is, first you put both your branch texture and your bark texture in one square texture. (You might have to scale them or crop them a bit to make it fit) Then you adjust the UV map of your model so that the branches are lying on the part with the branch and the barky parts on the bark-part. Now for the alpha, you make it so that the barky part of your texture is white on the alpha and your branches have the alpha they had before - a black rectangle with the white branch shape on it. That way your model is using one texture instead of two.

I don't think Maya can use the alpha channel of a .dds, and neither can hpl, so what you do is, you save the diffuse (= color texture) as dds and the alpha as a separate tga image instead of leaving it in the alpha channel. (You can select the whole canvas in the alpha channel and copy whats inside into a normal layer) You can then use it in Maya (transparency slot in the material) and in the material editor to create your opaque trunk and half-transparent branches.