There is quite a bit of literature on this topic in the "Graph Drawing" community.
Although the goal is algorithms for automatically drawing graphs,
several papers offer criteria which could be followed by hand. I'll mention two.
(1) Eades, Peter, and Lin Xuemin. "How to draw a directed graph." In 1989 IEEE Workshop on Visual Languages, pp. 13-14. IEEE Computer Society, 1989.
Here their 1st criterion aims for a downward flow, but the preferred direction
could be, say, rightward.
Then one applies the criteria in order: C1, C2, C3, each step refining the
(2) Gansner, Emden R., Eleftherios Koutsofios, Stephen C. North, and K-P. Vo. "A technique for drawing directed graphs." IEEE Transactions on Software Engineering 19, no. 3 (1993): 214-230.