yea, you can vaccumm it out to speed up the clean up. Gratz on the algae scrubber! It's the best thing ever.
Yea, when the algae is gone, the nitrate will accumulate. In turns, when nitrate rise, algae will come back. When you have an algae scrubber, it'll keep taking up the nitrate. Basically, instead of algae on the rocks, they are on your scrubber. So, no need to worry about them as long as you keep your scrubber clean every 7 days.