An easy way to do this would be to siphon out a little bit of sand with each water change. Its not a drastic change where you remove everything at one, but a slow change.
Also, the point of removing the sand bed would be to remove a place where nutrients could build up. If you left a nice sand bed in the sump, it would defeat the purpose of removing the sand from the display. The sand in your sump would just become a remote sand bed.
Another thing to look at is what you have in your tank so far (coral wise). Bare bottom tanks are usually best suited for hight flow SPS type tanks or lower flow softie tanks.
I doubt that the sand bed is the main cause of your problems though. How long has your tank been up and running? I would try adding some Macro Algea like Chaeto first to try to help use up the excess nutrients in your system.
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