Tools -> Global Raise -> Water Level will rise the water level by the specified amount. Works fine on the mola2x2a Mars data if that is what you are using.

Looking great. Very nice work there.

The fill in the street in the second one looks a bit repetitive though.

I put it in on Malajuri, off the coast of a small island. The map looks quite tropical, so I think this is the best fit.

Now in the atlas:

If you have the crop image to aspect ratio option on when exporting, you shouldn't get those white bars on the top/bottom.

It gets a bit more interesting when using the dungeon walls, since a regular floor mask would cover up all the unevenness of the stonework. But I am wondering if you could use TRACED to generate a polygon made up from the total area of both the floors and walls here, perhaps with a distance of -0.5 or something like that to make the mask "hole" for the dungeon to give that below ground feeling. Probably need to do something with the path to the entrance too though, to make it look like it is sloping downward towards the entrance.