I assume by "project board" you mean something like a breadboard or a piece of wiring board, (strip board, veroboard, perf board) for a finished project.
I usually try and lay the components out in a similar way to the circuit, so that there is a logical flow to the layout.
Usually with the best will in the world you can still end up with a mess of connecting wires.
Experience is the best teacher. You learn by your mistakes and think "I wont do it that way again!"
JimB