There are a couple of issues you ask here.
First is what happens to the difference (called a deficiency) between what you owe and what is netted at the sale. That is negotiable. Some banks will forgive it and some won't. The bank can pursue the deficiency debt for many years after the sale, so it is something to ask about before you sign the final short sale papers. One of the biggest advantages of doing a short sale is knowing how the bank will deal with the deficiency. You might have to agree to pay something to the bank to get rid of the deficiency. That amount is negotiable.
Second, typically the bank approves the payment of the commission but you will want to confirm with your agent what happens if they don't or if they approve less than the amount you contracted to pay.
Third, not making payments has a very negative impact on your credit, if that is still an issue to you. If you are not able to make the payments, that is something different.
Fourth, I don't agree with Tina that the bank becomes the seller in a short sale. You are still the seller and you decide if the terms of the sale are acceptable to you before you let the bank make any decisions about the sale of YOUR home. In a short sale, the bank is determining if they agree how to deal with your shortfall between what is owed and what you can get for it. You will appear at the closing table, not the bank. The deed will be from you.
It's still a complicated process and it can be frustrating. Make sure you chose an agent who is experienced in short sales and can provide you with the assistance you need while you navigate this sale.
Good luck to you.