I'm using quick lights, as well. The bottoms of mine don't seem to light along with the rest of the coal. If you aren't doing so already, make sure you blow on them for a bit until the entire thing is glowing. Try blowing on the black spots until they shrink and go away, too.
If that doesn't help then I don't know what else to tell you. Just make sure you are getting good air flow/heat and that your coals aren't acting up when you look away
I know the quick lights im using aren't exactly of the best quality. >_>
EDIT: Also note what Jilly said. I watched her video when I got my hookah the other day and since I've been doing two layers of foil it's helped a great deal.