When using a recorder with two microphones, recording from both microphones simultaneously means recording a single stereo file. A stereo file has two channels of audio data that can be played back simultaneously. In the case of recorded music, this would mean one channel being played in your left ear, one in your right ear.
After they are retrieved from your recorder, stereo files can be split into separate mono (single-channel) files using Kaleidoscope's free file conversion features. Under "OUTPUTS," simply check the box to include WAV files and select "Split channels" prior to processing your batch.