Most of my experience with DFF3d and sounders in general is for bottom mapping and understanding underwater habitat. Only recently (past couple of years) have I used them to view fish. I don't think the 3d water column presentation is a high detail presentation. I would arrange the screen to be split or have multiple screens to watch the triple sounder view, the 3d water column view, and section view. Each view provides useful data, that work together the provide a better understanding of what's down there, even if they don't all perfectly agree mathmaticly.
Also if there are multiple fish in the same depth, they may show up as one fish because of the echo timing as the boat goes by only sampling some of the water. If you are still you may find fish of the same depth moving to the side and be more evident in the triple sounder view or section view.