I have the onboard Sony mic on channel 1 and an external, phantom powered shotgun mic on channel 2. In order to record 2 separate mono audio tracks, to later be able to use as separate elements in a NLE, do I need to have the CH1•CH2 option selected or the lower option CH1 on the "Record Channel Tracks" switch? Does it matter? Does the first option automatically (and irreversibly) merge the record of the 2 mics into a stereo track?

In order to record 2 separate mono audio tracks, to later be able to use as separate elements in a NLE, do I need to have the CH1•CH2 option selected or the lower option CH1 on the "Record Channel Tracks" switch?...
Lower option "Ch1" will do what you want.
...Does it matter? Does the first option automatically (and irreversibly) merge the record of the 2 mics into a stereo track?
It matters! The first option records what is present at the channel 1 input on both channels.

This sort of thing becomes instantly recognizable when one is monitoring with headphones, recommended in all shooting situations when audio matters.

Thanks. Then what does the CH1•CH2 option do? Merge the recording of both mics into one set of stereo tracks?

Is there a way of separating them after the fact if something has been recorded in this format already?

Thanks. Then what does the CH1•CH2 option do? Merge the recording of both mics into one set of stereo tracks?The first option records what is present at the channel 1 input on both channels.

Is there a way of separating them after the fact if something has been recorded in this format already?
No. If you've recorded something with the selection of CH1•CH2 then you only have one source, one mic, recorded on both channels.

Where I'm confused is because I recorded some footage with the CH1•CH2 option selected, but in my FCP timeline each track shows different waveform patterns. But if they were recorded from the same mic, why would they have different patterns?

Sorry, I can't answer that one for you. Do they sound the same or like two different mics?

If you have a single mic cam set to Ch1 & Ch2, gain set to manual, and different settings on each channel then one wave form will look smaller than the other.

Like Seth said you should be using head phones.

I do this all the time at wedding receptions I have the wireless shotgun plugged into Ch 1 and the on camera mic on Ch2.

when shooting dancing and such I have the wireless on a mic stand picking up the PA on Ch1, and ambient sound on Ch2.

When they toast I switch to Ch1 & 2 and record on both from the shotgun. My assistant will move the mic to the most appropriate spot to get the best audio. Hope this helps.

It does, thanks Ron.