Well, if you hadn't learned already, always make sure you have the hammer grid set at incriments of a power (2, 4, 8, 16, 32, ect.), as for the growing reef part, I guess you could make a couple of models (XSI is free and was used to make most HL2 models, otherwise Blender or 3DSmax are a decent choice too) and make some animations for them, setting that they grow during the night along with whatever you'll use to make it night.