Don't disturb more than the top 1/2" of a sandbed. Deeper sand will have anaerobic areas, and if you disturb them they will get oxygen making them aerobic which will cause that bacteria to die which may cause an ammonia spike in your tank. Unhealthy anaerobic areas may contain hydrogen sulphide (sand looks black and stinks), which if released into your tank may cause the tank to crash.
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Originally Posted by Snaz
The display tanks without sand certainly have sumps that contain sand. You need that anaerobic environment.
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This is not true. Anaerobic bacteria also inhabit live rock, so anaerobic areas in sand are not needed. Very simply, anaerobic bacteria convert nitrate to nitrogen gas which off-gases from the tank.