I would not stir it up if you have a ton of bubbles, because you can literally gas your tank of too much organic materials are released. This is based off a experience of mine between cycling and adding fish. I stirred the sandbed and my nitrites/trates spiked.
90 Gallon Reef - 3 Blue-Green Chromis, 2 Ocellaris Clowns, 1 Kole Tang, 1 Midas Blenny, 1 Longnose Hawkfish, 1 Zebra Dartfish, 1 Algae Blenny, 1 Six-Line Wrasse
29 Biocube Reef - 1 Chalk Bass, 2 Black and White Clownfish, 1 Yellow Watchman Goby, 1 Fire Goby