That's exactly right. ReefMaster expects all shorelines to be closed polygons, and will close them itself if they are not. So create the sea shoreline as you have done, and then join them using a few points just as you have in your image. When creating the map, define a mapped area (red box, below)
that lies a good distance within this defined "shoreline" so that the outer limits of the shore do not provide zero depth values to the finished map (i.e. in the image below, make sure the difference between the red and green lines is greater than "max interpolation"):