Have you got some experience with mixers? It's kinda the same principle.
You could see winamp as one channel here. For each channel you can set the volume (here the winamp volume). But when you set the max volume for one channel on a mixer, it is not always as high as the other channels (even if they are set to max). That is where the preamp slider comes in for winamp. You can adjust the slider to boost or dampen the signal a bit when needed. This is in a lot of cases also a source of distortion if the signal is boosted too much.
The other source of distortion in most cases is the equalizer. Because what it does is boost or dampen signals in a particular range (frequency). Same as with the preamp.
Then there is the master volume or windows volume in this case. where the volume for the channels is like an input volume control the master is the output volume control.
About you sound image. I think in most cases it's best to adjust the equalizer of your HU. Some of the headunits already have filters built in, i.e. for subwoofer,... Best thing would be to filter the bass from the signal from you 6.5s. With some HU you can do this. If you would use the EQ in MediaCar you just alter the complete signal that goes to all your speakers.