You would enter only the rental portion on the screen asking for the rental portion of your mortgage interest.
Do not check the box stating that you paid more mortgage interest than is shown on your 1098 unless you did pay more than is reported on Form 1098. It is not asking whether you are reporting all of the Form 1098 interest on this page, it is asking whether you paid more than is shown on your form.
Then, when you enter the personal portion of your mortgage interest, you should check the box stating that the amount you are reporting is different from what is shown on your Form 1098. You will then be asked to provide an explanation for the difference where you can state that the other portion of mortgage interest is reported on Schedule E.
@Drod1
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