Ok my 2 cents worth.
When I make a DDS in Photoshop I create whatever image I want and make my background transparent.
Then I save as , select DDS, in the popup window I choose 3 which saves the alpha of the transperant layer for me.
Now when I reopen the dds it will be a white background but the dds knows it's transparent and when i use it in my mods it stays transparent.
Also remember in order to save it you have to make your High and width of the canvas the same, example : 512 pixels x 512 pixels
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