SKS 5; Tools, Preferences, Image Editors, check Convert TGA files to PNG before using image editors.
SKS 6; Tools, Preferences, Advanced tab, uncheck Do not convert TGA to PNG.
Then when you edit a TGA image it will open in graphics app as a PNG with proper trans/alpha.
But what if you wanted to edit already created TGA files?
I save all my .png images in a seperate folder. If i need to tweak, I just open that image and fix it up, then reimport it. For some reason, in SKS, I can't use the edit image option. It wont automatically open GIMP for me, so I just leave GIMP open and switch back and forth between that and SKS.
Yeah, I do the same for my own skins since I work primarily from Fireworks. It makes it easy to tweak little things in future if you have the original files.