I haven't updated in a while. Here's a huge email I sent to another worship leader with specs on how we use videos with multitrack audio to get click, cues, and stereo loops (or even more combinations) synchronized with video.
We do this all the time at UCC now - it's our favorite way to present videos that have to be perfectly synchronized.
It does have a learning curve to create the content and to set up your system to do it, but we have found over and over that it is worth the investment of time and energy.
ProPresenter 6 can playback videos with multichannel audio discretely onto an audio interface of your choosing. I've used a Scarlett 2i4 for this also, but we now use Dante Virtual Soundcard to send up to 8 channels of audio to our Rio Dante input device.
We use 4 or 6 channels of audio (2 or 3 stereo pairs) within our videos depending upon how diverse the audio is. Usually it's just 2 stereo pairs - click track, cues, and stereo loops.
Here's a video that you can test that has 4 channels of audio. If you connect an interface to ProPresenter and select it as the output, it will render the audio onto the interface in order - click and cues (split left/right) and loops on the second pair.
We use Final Cut to export the videos with multitrack audio. You assign the audio tracks "roles" and export them. These screenshots show you how to do it.
First, you will put your audio tracks into the video.
For us, that is click track and cues (click panned left and cues panned right) and stereo loops. Then you assign roles to those tracks. For the click and cues, we put them into the role of dialogue. The loop (audio you want to go to the house) is assigned the role of music. If you have any panning, you'd want to designate that in the inspector window. We pan the click left and the cues right so they have different outputs.
Once that is done, you select File --> Share --> Master File.
Then in the export settings, you select Roles as Multitrack Qui
Then, you take this video over to ProPresenter 6. (It has to be ProPresenter 6, by the way...) You then select 4 channels in the advanced settings in ProPresenter. It should then map your video to your audio interface in order (the pair listed on top will be 1-2; the pair listed next will be 3-4, etc.). Make sure that the interface is selected as the sound output in your mac's system preferences.
In ProPresenter, you also need to make sure that you enable as many audio channels as your video has. This is in the advanced tab. You just select it. (Try restarting ProP after selecting this setting).
One other trick we use to make this work like normal ProPresenter songs is to make the lyrics "off screen" for the stage display. If it's a video in ProPresenter, there's no need to advance slides since the lyrics are (usually) part of the video. But, if you want lyrics, you have to have them off the screen so that ProP can read it for the stage display, but won't output them over the video. We made a template that moves the text box for lyrics to be moved off the screen. I can give you more directions if you have trouble with that part.