If you are already late on your mortgage payments then the damage has been done to your credit rating. Typically other credit, such as credit card limits were reduced or closed entirely on you by now.
There is only one way to protect a credit rating prior to defaulting on a mortgage. Before you defaulted you would need to send the lender a "qualified written request" and then if you default in order to execute a short sale and the lender does report 'late payments' on your credit reports, this becomes illegal for the lender and they actually owe you money! Furthermore, the lender must remove those late payments. Understand that in the end the 'short sale' will remain on your credit reports however all the 'late payments' will have to be removed by the lender.
For the future, your credit rating will be much more favorable if you have a short sale that does not include late payments, vs. a short sale that does have late payments. This strategy works well for Foreclosures, Deed in Lieu and Loan Modifications as well. Good luck!