I'd keep the filter going 24/7 for a couple days. You should be brushing the sides and bottom to loosen up the dead algae and getting it into the water where it'll be filtered out. It may cloud up again but that's good, the filter will get it out.

Watch the pressure guage for it to rise which will tell you the pump's working harder to push water thru the cartridge. That's when you should pull the cartridge and clean it.

Once it's all cleaned out you can cut back the time it's on.