Mark, does this mean I wouldn't have any output coming from the HU to the
stock rear speakers? If the rear output of the HU goes to the front
speakers and the front output of the HU goes to the sub, how could I power
the rear speakers?

You run the rear output to the rear speakers as well. The line out
converter or speaker level input to the amplifier (whichever you decide to
use) is a high impedance load and won't draw much current from the head
unit, so it's ok.

Also, this sounds somewhat complicated to me. Would an installer from
Tweeter or Circuit City be able to do this without getting confused?

Yes. It's simple. You could ask them to run the main speakers out of the
front channel and the sub out of the rear, or vice versa. It doesn't matter
which. Just as long as you make it clear to them that you want to be able
to use the fader as a sub level control without attenuating the rear
speakers in the process. If they tell you that it can't be done, then
they're morons and you should probably go somewhere else. For what it's
worth, Tweeter hires better installers than CC. Although I know of a couple
that are chock full of fools.