As long as the intake is not too low sand does not get up into the filter.
If you have fish that dig, then you might keep the intake high enough that they won't kick up the sand that high, and put a coarse sponge over the intake.
I only had one tank where the fish rearranged the substrate that much, it had Botia kubotai, but I also had the intake quite low, so it may not have been entirely the fault of the fish. The substrate was coarser than sand, and all it did was to clog up the sponge over the intake. Other species of fish dig a lot more than these guys. Yoyos and Clown Loaches seem to dig the most, IME, but none of them can match certain Cichlids for the amount of digging they can do.
Happy fish keeping!
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