If you file Chapter 11 protection it will affect all of your assests (first and second mortgage). Prepare to lose your 2nd property, you won't be able to keep it.
It depends on the type of bankruptcy you file. Chapter 13 sets up a plan to pay back your debit. You will still be required to make you mortgage payment. Chapter 7 eliminates debt but will not guarantee you keep your home. Filing bankruptcy may give you time to not make payments and find the best option for you.