If it is really green and swampy, you can vac to waste. However, that wastes a lot of water so if it isn't so bad, you can just vac to your filter and then backwash when you have the pressure rise. Your call on that one but at any rate, continue to keep the chlorine high. If you pour the bleach directly into the skimmer (while the pump is running) it will kill any algae in the filter.