OP is right. The components cover each other so you can't see what's where. It only works if it's a) 2D or b) the parts are translucent so you can see through them or c) you can move/rotate the breadboard to see it from different angles.
Old_Grey talks about learning tricks. Those tricks are more properly called workarounds and imply that the software is flawed in some way. These are problems for low part counts.
That said, I'd suggested planning a circuit first as a straight forward circuit diagram before planning it on breadboard but that's just me and I don't do this often.