I was just about to post something similar to Albert about the rocks-sand.
I think you said your sand bed is 2" right.
A shallow sand bed should really only be about a 1/2" of sand that you can clean with a siphon to remove any detrious on a regular basis.
A deep sand bed should be 4 - 8 inches deep to get any of the benefits of the nitrifying bacteria.
Since you are in the middle, you get none of the benefits and all of the problems.
As for the rocks, I would check with albert and take his advise on stacking them. If you went with a deep sand bed, it would not be as big of a problem though.
Anyway. My 2 cents.
