IPhone – Can we use only the bottom mic while recording audio using iPhone 6

There were no devices which were designed to filter matching audio into two iOS devices at the same time. The solution I went with in my comment is likely the best.

That is, Adobe Premiere and Final Cut Pro X both have a feature which will use audio to automatically sync up video tracks. I recorded high quality audio with an external microphone, and using that in conjunction with the audio built into each device, FCP:X was able to create a multi-camera clip with the three audio tracks and two video tracks synced up. I could then select each audio track and each video track independently.

Rogue Amoeba's Loopback will allow you to route virtually any input/output to/from any Mac application. It is easier to use than Soundflower, and you can create multiple routings (which Soundflower does not) -- but it is a paid (and supported) app (unlike Soundflower).