You should start GRADUALLY raising your chlorine level using cal hypo* added to the skimmer, to the 5 - 10 ppm range, while watching to see if stains reappear.

Meanwhile, continue to use polyquat regularly. Until your chlorine level is over 5 ppm, it won't be safe to depend on chlorine alone to keep your pool algae free.

PoolDoc

*All previous cautions about the dangers of doing this still apply. This is safe ONLY if you 'follow the rules'!