Yes, for your rental mortgage interest, just report this under your rental section. Any portion that is not available for your Schedule E will automatically go to Schedule A (on one of your rental properties).
It is important to note that for the mortgage interest deducted on Schedule A, you are only allowed an itemized deduction for your main house and ONE additional residence. The IRS does NOT allow a personal mortgage interest deduction (on Schedule A) for more than TWO homes.)
If you enter it in both places, your deductions will be counted twice.
