I don't believe support for multiple skins is available in PAHUD, though the stats should appear right you won't be able to see the skin in the PAHUD layout manager.
Well, there isn't an automated way to do that I'm afraid.
If you don't mind getting your hands a little dirty, you can replace the C:\Program Files\PokerAce HUD\Data\Images\table_ps_x.jpg images with images from your own theme. It appears that's where PAHUD reads those images from and if you change them to match your layout you'll see your layout there.