I when I listen to songs and want to figure out what chords are being played, I constantly have trouble... Single notes are somewhat easy since i can traces them down...

The pickup setting, I can only hear a big difference between the bridge and the neck pup, but the other 3 settings dont sound that much different to me...

How can i make it better... -.-
Listen to simple chord-based songs, like Stadium Arcadium and Wet Sand by RHCP, learn the chords for em, and that might help a little. At least youll be able to figure some stuff out.
Practice. Listen to alot of music, and try to listen 'active'. There's really no easy way to develop an ear, you just have to play and listen and eventually it will come. A good idea when listening for chords, is finding the root tone, and you can almost always hear whether it's a minor or major. By finding the root and using your knowledge about scales and the circle of fifths, it's piece of cake to find the chords.