Having 2 mortgages is not a problem doing a short sale it's just twice the amount of negotiations. You have to get both banks to agree to a payoff amount. Get a number from the first and negotiate like crazy with the second. A good rule of thumb is that 2nds like about 10% of balance but I've seen them take as little as a $1000. They won't get much from 1st (if anything at all) if the house goes back to 1st bank.
Give me a call I can help walk you through the negotiations or if sellers are just trying to do it alone I can help whether it's listed for sale with a Realtor or not.