You really DON’T want to use the headphone output and the Mic Input to
record professional sounding audio. This is a decidedly Lo-Fi approach.
You want to use the L/R Audio Outputs on the Back, or the L/R outputs
of a mixer, and run them into a mixer or the L/R audio in on a computer
sound card.
Anyway, you probably *could* use the headphone out (but the Signal To
Noise ratio and harmonic distortion are not as good as the back outputs),
but if you are only getting one side, or weird cancellations, then you are
probably not making correct contact with the pins of the headphone jack.
Or you do not have the correct cable. The headphone Jack is a mini
stereo T/R/S (Tip/Ring/Sleeve) - if you are not using a stereo T/R/S
cable, you will only get one side - or worse, a weird kind of phase-inverted
sound.