In more detail
The node network lays itself out to start with. Custom placement lets you drag themes and codes to where they make sense to you, for example grouping themes you plan to discuss together. In the hierarchy and file tree it lets you reorder themes and codes.
A bubble moved in any mode other than Work springs back, so arranging is always a deliberate step.
In Themescape
Switch to Work mode and use Custom placement. Each view keeps its own arrangement. When you save your progress, the arrangement goes into the layout file, which is the only way to keep it between sessions.