The 1031 is just telling the IRS that you swapped one for two properties. The fact that you are renting them versus another use, means that you must input them into the rental section. If the properties are a duplex type of item, then combining them could make sense and selling one later would be a real hassle. If they are two distinct properties, you need to enter them separately. On the bright side, once you enter the first, the second will go quickly.
The Instructions for Schedule E (Form 1040)state: Complete lines 1a, 1b, and 2 for each rental real estate property.
@darmendarez
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