You can try the following approach. Start by arranging your diagram with "Layout" -> "Flowchart". Then manually move nodes whose positions you do not like to better places. You do not need to place them pixel perfect, just in the rough vicinity of a good position. Then run "Layout" -> "Hierarchical" with option "Use Drawing As Sketch" activated. Maybe you need to set strong port constraint before the hierarchical layout run as well to keep the original edge connection points. Port constraints may be specified using "Tools" -> "Constraints" -> "Port Constraints".