My experience with algae scrubbers (both waterfall and upflow types) is that there are always bits of algae floating around in the main/display tank. If you're using a sump, you could run the return through a filter sock or something similar to catch it before it gets back into the main/display tank. I've never had any problem with algae growing in my main/display tanks, possibly because the lighting is not very good for algae growth. What little grows usually goes away on its own eventually since the scrubbers out-compete it for nutrients.