separate channels?

It looks like I'm able to customise some arguments to the sox command by passing fake input filenames, but how can I pass arguments, e.g. remix 1 after the output file?

E.g. replicate this command

sox file.wav -b 16 -r 16k output.wav remix 1

[igece]

To pass customized arguments you should use the CustomArgs property of a Sox instance. However, what you want is to use a still unimplemented effect (remix), so in this case the property you should use is CustomEffects, setting it to "remix 1".
The difference between CustomArgs and CustomEffects properties is that the content of the first one is placed before any input argument, and the content of the second one is placed after all the output arguments (where effects are passed).