Use a USB sound card with multiple input lines in apps like Skype or Dictation?
In Audio Midi Setup, you may have the choice of which is the primary input in non-ASIO applications…



Alternatively, it might be possible to rearrange the inputs if you use an Aggregate device 



I've only used Aggregates for testing, experimentation, so I'm no expert - but it appears you can renumber the channel order by clicking the individual channels in the top section.