Technical (process flow) diagrams can be mess with intersecting and overlapping arrows. The challenge of the presentation designer is to unravel them. I usually decide between 2 possible solutions:
  1. Minimal clutter. Like unraveling physical wires, I re-draw and re-draw the diagram again until I have it in such a configuration that none of the connectors overlap (or with the minimal overlap). Then I resize boxes to the same size, align and distribute so that the whole thing lines up nicely in a grid. The result is pleasing for the eye.
  2. Maximum logic. I take the big steps in the process and line them up in the logical sequence. Other intermediary steps get organised around this. Use differentiating color for the main big steps in the diagram. The result is pleasing for the brain.
Then decide whether to please the eye or the brain.