I agree with the filler option as this the method I prefer to use myself. I place the landmarks 1 block above the water and let the fill do the rest. It will place the sand blocks in the air, since there is nothing to hold it up the sand will fall and be replaced by the filler automatically. The only issue is supplying enough blocks to fill your cuboid space. If you wish to preserve the topography of the ocean floor then I suggest using gavel instead. It will make it easier to see how much to dig out. The only down side of gravel is it can be a pain to source enough to do the job you need, whereas you can easily make sand with an igneous extruder and pulverizer setup.