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depends why the sand is turning black, ... get stuff to burrow in your substrate, ... either worms or snails (or something i haven't heard of yet)

black is a sign it's not getting enough Oxygen , ... yes that's bad near the surface, ... otherwise it's normal decomposition and being in the substrate, as aokashi said, it's not normally a problem otherwise. ... trust experience more than theory, aokashi seems to have experience :)
 

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the kuhli loaches at your LFS, ... the gravel the store was using, ... i'm assuming large gravel, large enough for the loaches to find paths through it, ... large enough that considering if the loaches found a tunnel of sorts.

finding a tunnel is different from digging to burrow.
 
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