I have an audio and a MIDI track with Record turned on, and at some points in the audio track, I want to Mute the track and turn off Input Echo during recording. However, the Manual Mute won't work, because I can still hear sound coming through on the audio track while I leave the MIDI Track on. Is there a way for me to fix that so I can mute the audio track while recording MIDI from the Virtual Instrument track? If so, how would I do this?

Use Mute automation. 

bitflipper
Use Mute automation. 

I've tried that, but I still hear sound from my microphone when I play back the results. Funny it works when I record, but upon playback, that's where disaster strikes.

Are you monitoring through your audio interface? If so, you'll have to mute the mike channel at the interface itself; it won't do any good to mute it in SONAR.

bitflipper
Are you monitoring through your audio interface? If so, you'll have to mute the mike channel at the interface itself; it won't do any good to mute it in SONAR.

Unfortunately I'm not sure how to mute the mike channel at the interface. I don't know if I would do it within Motu Audio Console or Motu Cuemix FX, as the UI is made so I can't see what's on the screen. In other words, my screenreader can't read all of the parameters. What do I do next?

Sorry, I forgot about your reliance on a screenreader. I'm trying to think back to when I was using CueMix, if there were any keyboard shortcuts for muting channels. Perhaps someone who is currently using a MOTU interface can suggest a solution.