1. Yes, your rent payment went through
2. Yes, you need to bring back the account into the positive, including the overdraft fees. You have 6 days to do this, since they charge for overdraft fees every 7 days (each item)
Once you overdraft, you cannot get the money back
First off, get online banking so you can review charges, and pending charges!
ISF USUALLY means they paid the transaction.
You will not get the ISF fee back. You should be sure your deposits cover the fee and the balance shortfall or your account will remain in overdraft and you will continue to be "hit" by ISF or return check fees for any pending / further debit transactions.
1. Did you pay your rent using a debit card or with a check? Do you have an overdraft privilege? Lots of things matter here. If you paid with a debit card and the transaction was preauthorized (your card worked), under REG E the bank has to pay it. You cannot return debit card transactions, but they can be rejected on the spot.
If, on the other hand, you wrote a check and it was NSF, yes, it definitely could've been returned. You will still get the NSF fee, and your rent won't be paid. Like I said, though, many places have overdraft privileges. For instance, where I work, you can have a $500 ODP on a free checking account. If your rent was $600 and you had $100 in the bank, the check would go through (barely, and if you had nothing else going through).
2. No, you will probably not be able to get the NSF fee back unless it's your first time. What you have pending means nothing. What is posted is all that matters. Go and talk to a personal banker about your account... and what opting-in and opting-out under REG E will do to help you. Without knowing if you use checks, how much (if any) overdraft privilege you have, or anything about your spending habits. That's why you go see your banker.
I could watch Schnidler's List and still be happy after reading this.