I don't, my substrate is sand as well... The poop just sits on top of the sand, and it vacuums off very easily. I can get the tip of a siphon hose down in the crevices of all my boulders and I siphon the poop out of there pretty good too... I have the power-clean attachment for my HOT Magnum intake, which I use to get in the crevices before cleaning my filter also.
I would imagine you maybe able to clean the shells with a turkey baster, without having to remove them? Maybe you could blast some water in there and get the poop/mulm out before a substrate cleaning?
I manage to suck up lots of sand when I clean, but really this is no problem because I just leave the sand in the bottom of the bucket, rinse it and put it back in the tank... But, the boulders in my tank are too big to move, so I don't really pull them to clean around them.
