I always end up making two diagrams, a schematic and a layout.
The schematic has to be easy for me to follow the action. I arrange IC pins any way that suits. As I experiment on a breadboard, I usually re-draw the schematic.
When I'm ready to solder, I work on the layout, arranging components so their leads meet as conveniently as I can manage. IC pins match their real arrangement. I usually re-draw the layout a few times.
I would have trouble doing the whole thing in one diagram. Even more trouble if I were to use microcontrollers, projects with buses, etc.