Need advice on how to handle this rent situation?

Talk to the landlord about your situation, If you have been a decent tenant and still truly carry a positive balance with him in the form of the security deposit he should be fine with just withholding the portion of which you owe from your original deposit as long as the home is not left in a state other than it was in upon your move in. Another thing to consider is re-read your tenant lease. Most landlords require first and lasts months rent upon move in as well as a security deposit for damages that may occur. All deposits are refundable if damages have not occurred. So in short, he may just work with you. But only if you man up and explain your situation, your deposit is in place to cover situations such as these. If he does not work with you then you may still rest easy as your deposit covers any final damages weather physical to the home or through non payment. Keep in mind if you stay for a longer period then the amount you have as a deposit can cover you can then be sued for compensatory damages to cover the rest.