If you are using TurboTax for Desktop, you can track the amount on Schedule E in Forms Mode (click the Forms icon in the TurboTax header). Open Schedule E Wks for the property and scroll down to Line 12. Above Line 12 is the Mortgage Interest Smart Worksheet that should display the source(s) of the interest on Lines 12a and 12 b. If the loan is split between Schedule E and Schedule A, the allocated amounts will appear in columns (c) and (e).
If you're using TurboTax Online, you will need to review your entries for mortgage interest in the Rental Property topic to verify the interest was entered only once.
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