I agree that the black and green your are seeing is probably algae stains as nefretramses mentioned. You can try bringing your water back up to shock level (10+ with 0cya) and getting some on the affected areas and hitting it with a brush some more.

As far as the cya you've added not showing up, according to my calculation on an 18.5k gallon pool that 4 lbs is only going to get you 26ppm cya once it's fully dissolved. I wouldn't bother with polyquat while shocking, the chlorine is just going to eat it along with the funds in your wallet.

For your question about circulating chlorine with no pump. Use a stick, brush, or other tool to stir up the water and mix it in. Do your best to pour it in different spots and/or mix as you go. If you pour a bunch in one spot and don't mix it you might lighten your liner in that area.