I siphoned mine out with each water change. I have less microfauna without the sandbed though. I had buttloads of little critters before I removed it, and now I don't notice any. There's a little in the sump, but not much.
The BB is much easier to maintain though, and I was also having the clumped sand syndrome, since my opened top won't keep any gobies in.
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Everything I put in my tank is fully dependant on me.
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