You can aggressively scrub LR as long as you do it in salt water. If it's not covered in Coraline I'd recommend it. You may want to soak it in hypersalinated water to drive out worms and mantis shrimp.
Start skimming immediately. As "stuff" dies off the rock you want to skim it out. IMO, a good skimmer is one of the most important parts of your setup. Choose well and go for overkill. There are lots of threads on skimmers floating around. Do a search.
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300 Reef; 325LR, 1/2" sand bed in tank, 3" sand bed in 215 gal sump/refugium and Berliner PowerPro SS twin becket skimmer. 210 Reef; with 225 lbs of LR, 300 lb DSB, Large W/D and Jebo 520 skimmer modified to accept a becket. 90 RR FOWLR; tied into the 300's sump with a closed loop for extra circulation. 55 hospital. | 
