If I put my 30 day notice in, I only owe a prorated amount of the rent correct?

Yes, you should be pro-rated through the corresponding day of the next month. And no, if the damages are higher than the security deposit, they can come after you for the difference. The security deposit is there for a minimum level of security for the landlord (meaning at least he/she will get something for the damage) but it does not mean that that is all you might owe. Before leaving, take pictures of the apartment so that is they try to charge you are other stuff that was not there, you will have evidence.