Unwanted Arrange behaviour in GraphEdit

Ok so I kinda understand them now, however there seems to be one big issue:
When clicking the "Arrange" button, it seems to arrange the nodes based on which layer they are (those get "stacked" over each other). The problem is that that obviously discards the relationships between the nodes which causes the graph to look like a complete mess. I assume the only option I have is to write my own "rearrange" code but I don't really have any idea of how to approach this. Any help is appreciated

#Unwanted Arrange behaviour in GraphEdit