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Good question. I'm currently doing that by running multiple instances of ffmpeg at the same time. If I could do them all in one command, that would be really nice.
I believe the basic format you likely want is ffmpeg -i input1 -i input2 -map 0:v -map 0:a -c copy output1 -map 1:v -map 1:a -c copy output2, where ex. -map 0 corresponds to the first input, -map 1 corresponds to the second input, etc.
ffmpeg -i input1 -i input2 -map 0:v -map 0:a -c copy output1 -map 1:v -map 1:a -c copy output2, where ex.-map 0corresponds to the first input,-map 1corresponds to the second input, etc.