1st off, sound stage is the ability of a system to accurately reproduce the music as it was originally performed - I don't know about you, but when I go to see live music, I tend to face the direction the sound is coming from - hence the importance of well installed and set-up front speakers, and the reason that 6x9s aren't used by sound quality enthusiasts.
Human ears are very sensitive to higher frequencies, and good at locating the direction the sound is coming from - another reason to have your detail playing in front of you. Lower frequencies (those played by a sub) are not so easily located, so playing sub 100hz frequencies in the boot is not a problem, and won't upset your sound stage. By having full-range speakers behind you, you are destroying the stereo imaging of your music.
Now for your amp - it's a GTH400, and looks like a nice bit of kit. This may be of help to you:
http://manuals.harman.com/JBL/CAR/Owner%27s%20Manual/GTH400%20om.pdfIt should help you get an idea of where your settings need to be. If you wish to use your 6x9s, and don't want a sub, you could always low pass them - just sent them the lower frequencies.
The gain controls are there to allow you to match the output of your headunit to your amp. You can either set them up the teccy way using an oscilloscope, or the loud way, using test tones. Or you could just set them at half way and hope for the best!
L stands for left only (poss for a sub input), ST for stereo, and L+R is probably for left and right combined into a mono signal - but that should all be in the manual. Hope that helps!