How to rescape an established tank

[Amandas tank]

I have rescaped a small 20 gallon tank before, but now I have a much larger tank with bigger fish. I am not sure how I should go about rescaping it. I need to add more substrate, and I understand that messing with substrate will kill off beneficial bacteria. So, I am thinking I need to do one side at a time a week apart. Is this right? I also will be adding driftwood and various sized rocks. And later, more plants. Will I need to wait to add the hardscape or can I do it as I work on the substrate? Can I do this safely with my fish in the tank or do they need to be removed first?