I would worry about that drain on the bottom of the sump. I'd seal it.
And the sand can sit until needed, then used as-is. No more mess than the added rock. All the ammonia will be gone by then.
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Inventor of the easy-to-DIY upflow scrubber, and also the waterfall scrubber that everyone loves to build:
http://www.reefcentral.com/forums/showthread.php?t=1424843
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