I am trying to record two USB mics as separate tracks on our MacBook Pro. I don't want to purchase an expensive mixer, as I don't have the money. I'd also rather not have two separate programs running, just one. How do I do this?
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The traditional way to accomplish this is with a multichannel audio interface. It doesn't have to be a full-on mixer, but it does need to have more than one input channel. PreSonus makes good-quality, reliable, and relatively cost-effective solutions for this. Note the two XLR connectors on the front of the interface. You will need two traditional microphones and XLR cable. The USB microphones you already have combine a number of different components: the microphone itself, the mic preamp, and the audio interface. This allows you to do one thing and do it well, but limits you in the long run in terms of how flexible you can be with how you use them.
After you have the right hardware setup, the software shouldn't be too much of an issue--in fact, the current version of GarageBand has support for multitrack recording under Track -> Enable Multitrack Recording. Then just set your two tracks to the two channels of input on your interface and go to town.
In OSX, multiple audio devices can be combined into one "logical" device in software by creating an aggregate audio device. The link is for 10.6, but it should be basically the same thing in any other OS. All this does is allow separate interfaces to be addressed as separate channels in a recording program. It does not guard against phasing or jitter issues or any other inconsistencies between your devices.
Now, the comments on NReilingh's answer suggest that you don't necessarily have two separate USB audio devices, but rather just want to hook up two ordinary mics without a mixing board. If this is the case, then his suggestion of a multichannel audio interface is generally the best approach. Think of it as one USB adapter for both microphones at once.
One of the possible solutions is to use ffmpeg
Two stereo microphones will produce a WAV file with 4 channels.
File opened in Audacity:
To list devices:
Example batch file
for this job:
Drop it to ffmpeg.exe folder and run in cmd window:
Console output(empty lines added):