Oh yeah by all means try not to do a big wall of rocks. But you want a nice stable platform with a plateau so to speak at the top under the lighting. Preferably in the center if you want it to be a centerpiece.
All my upgrades I just transferred all rock, all water, and topped off with fresh saltwater matched close to my old water. Never had an issue or a loss. But like I said above I wouldn't risk a new mag to a mini cycle if you have one. If your rocks aren't out in the air for long you should be fine. Always ditch the old sand tho. Nitrate bomb waiting to happen.