Hello @kbsitz:    Here is a link to a post I did on security deposits.   You will basically show the entire deposit but add a line item for the security deposit.   The security deposit will be a liability account.  

I hope it helps.  If you have more questions, feel free to reach out.   Real Estate is on of my favorite topics and I have many customer's that have this type of business, including my own properties.

Lynda