SourceCapturesShortcut
MicrophoneYou⌘⇧M
System AudioEveryone else, and anything else your computer is playing⌘⇧A

Both are on when a recording starts, and both can be switched mid-call. Turning one off does not end the recording; it just stops that half being captured from that moment.

Changing microphone

The chevron beside the microphone control lists your input devices, with a tick against the one in use. Switching mid-call is fine. Junior follows the change without interrupting the recording. Settings also has a Microphone Device preference if you always want a particular headset.

What "system audio" really means

It means everything, mixed together. Junior takes one feed of whatever your computer is playing: the call, a video you share, a notification chime, music you forgot to stop. It cannot isolate a single application and it cannot exclude one either, on either platform.

In practice: mute or quit anything you do not want in the recording before you start. See what Junior can and cannot hear.

Questions

Can I record only the other person and not myself?

Yes. Turn the Microphone off and leave System Audio on. Your voice then does not appear in the transcript at all, which also means your questions do not, so an interview reads as a monologue. Usually not what you want.

Can I exclude one app, like my music, from system audio?

No. Neither macOS nor Windows lets Junior take a per-application feed, so it is all or nothing. Stop the other audio before you record.

Won't my voice get recorded twice, once by the mic and once through the speakers?

No. Junior removes the sound of the far end coming back through your speakers from the microphone channel, so remote speech is not transcribed twice as if you had said it. This is why your own words land as You and everyone else lands separately, even on a speakerphone in a room.

What happens to the transcript if I turn a source off mid-call?

The transcript simply stops receiving that side from then on. Everything captured before is kept, so you end up with a call that has both voices for the first half and one for the second. Junior does not warn you about this, so remember what you switched.

Junior says system audio capture failed.

Something went wrong grabbing the system feed, and other speakers are not being recorded. Junior says so in a banner and suggests switching your output device in your operating system's settings. Do that, and check Junior cannot hear anyone if it persists. Your own microphone keeps recording throughout.