Are you just using an AUX input?
Have you tried tweaking the settings on the equalizer on your phone? Not sure exactly where it would be on your Note 2, but if there isn't one built in, you can use the Google Play Music app, or Poweramp, both those have built-in EQs.
Also, if by "muffled" you mean distorted, turn down the volume on your Note a couple of notches. My personal experiences with many phones and headunits is that if the device plugged into the AUX input is cranked all the way up, it will really degrade the sound quality.