sand bed question

So I'm setting up a new system and need some opinions......is it better to stack your rock on the bare bottom of the reef tank or to put the sand in first then stack the rock on top. I plan on have some diamond gobies but don't want a lot of sand on visible on the front of the glass/viewing area. Do the diamond gobies need 3" sand bed or don't they need that much? Does the whole bottom of the tank need to be a sand bed for the gobies or will they be fine with just "perimeter" sand in front of and around the rock? Thanks for the help.
 
when i set up my 240, i put down egg crate (light difuser panels) then i layed my rock on top of that. last, i put my sand in.

this way, my rock was not sitting on my bottom glass. (i have a glass tank by the way)
it keeps my rock off the bottom, and keeps things from digging under the rock and having them fall over. (break the glass and go swimming.......)

thats just what i did, but im sure there are other ways to do things.
 

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