Security deposits are recorded with the leases information. Go in the Tenants menu, click the tab Leases, then click New in the right side menu and enter the appropriate information.
To get a list of your security deposits, use the security deposit related reports.
When cashing out the security deposit (interest paid, money's owed, etc.) we suggest you to only enter in the difference because the rest is just considered a deposit and not a revenue. As well by going this route it separates out your "real" revenues from your deposits.