First, you will need an application that can save images with transparency. If you have photoshop, great. Otherwise, try GIMP. It's free, and is very powerful.
Link to GIMP:
http://www.gimp.org/
Next, open VTFedit and then open your image. Form there, save it as a VTF file in the folder C:/program files (sometimes 'program files (86)')/steam/steamapps/common/Portal 2/portal2/materials/(custom folder name).
Finally, in VTFedit, click File>New and then you should see some text area. replace whatever's in there with
"LightmappedGeneric"
{
"$basetexture" "[Folder]\[overlayname]"
"$decal" 1
"$decalscale" 0.25
"$translucent" 1
}
(I probably screwed something up in that code because I copy/pasted that from a Counter-Strike forum. It works for me, though.)
Under $basetexture, change [folder] to the folder you created and [overlayname] to the name of the .VTF. Save that as a .VMT in the same folder as your texture and you should be good to go! Be sure to Pack your texture into the BSP before releasing the map, though.
EDIT: Oops, Need to put a link to VTFedit. http://nemesis.thewavelength.net/index.php?c=178