Here is some advice that I believe should help to reduce distortions when recording:
First, go to both your recording device and you speakers and go to the levels tab. Afterwards, right click the percentage and switch it to decibels. Then make sure that the device is not adding or subtracting decibels(I recommend plugging in the Noise Filter to your PC to avoid having your computer blast the audio,
The next thing you need to make sure of is to make sure that your PC is outputting to the maximum possible quality as well recording it. Select the largest number of Herts as your sample rate as well the preferred bit depth.(Do this for stereo mix as well).
Something important that you need to remember is to make sure that you have an AUX/3.5mm cable in your 3DS when recording to maintain minimal distortions.
Now for the obvious portion; if the slider is present on the 3DS Capture Application, slide it all the way up!
Well good luck everyone!