Last year, the two editors were merged together into a single map editor. A majority of the useful tools from the devkit are available in this editor, along with all of the things the devkit wasn’t able to do. You can create volumes (and paint terrain holes) in this editor.
Landscape hole volumes are deprecated – you shouldn’t/can’t use them. Holes should instead be painted with the terrain tools. Terrain > Materials > Cut [R]
If you’re underwater and you’re not near anything (e.g., the sea floor or other terrain, objects, etc.) the only thing you’re going to see is the water / air bubbles.
You could use the snap tools. Set the snap value in the bottom-left, and then use the snap tool by holding [Ctrl] while moving/rotating the object. E.g., you could set Snap Translation to a small number if you wanted to move the object very precisely.
If you don’t want to use the snap feature, note that the movement tools follow your cursor. If you move your mouse slower (or faster), then object will also move slower (or faster).
If it hasn’t been placed as a Water volume, then it’s likely the default water. You can add "Use_Legacy_Water": false, to the map’s Config.json file to remove all of the default water. Then, you can re-add water manually with the water volume.
For example, the Config.json file would look like this, if you don’t already have one:
I tried to take a look at this today, but I think you’ve taken the mod down sometime between the weekend and today. As such, I am not able to look at this right now.