Leave fish in there... no need to stress em' out any more than you need to... Just make sure you don't squish em' LOL Corals... If there getting in the way take them out, they'll probably close up anyway... just keep em' submerged, and don't let the water quality in whatever your putting them in deteriorate... and they should be back to normal the next day.
Try to keep your rock structure on the narrow side, to accomodate the dimensions of your tank, and try to keep an open rock structure - this way the water can flow through the rocks easier, eliminating dead spots where detritus will settle, meaning better water quality since more detritus will make it to your skimmer.
