You are exactly right. If you switch between skins, the button colors will be different, so SaT will not know what to look for. So you will need to Remove and re-Include the WinningPoker site each time you switch.
One workaround is to have separate layouts for each skin. Just use File->New Layout, and use the same table size as your previous layout, and then set everything up the same. Then, depending on the skin you want to play on, just use File->Open Layout, to make sure you're on the correct one
As for Jackpot tables, you also would have to include the other site in SaT: WinningPokerJackpot
One workaround is to have separate layouts for each skin. Just use File->New Layout, and use the same table size as your previous layout, and then set everything up the same. Then, depending on the skin you want to play on, just use File->Open Layout, to make sure you're on the correct one
As for Jackpot tables, you also would have to include the other site in SaT: WinningPokerJackpot