1. Every time a dialog is created there is a recourse created in the same folder with _graph.res in the end of file name. For example: we create a dialogue named MyDialogue, we will see a folder created at res://game/dialogs/my_dialogue/. Inside that folder there are files

       my_dialogue.gd
       my_dialogue.tres
       my_dialogue_graph.res
   

The file my_dialogue_graph.res is the graph file. It is empty after dialogue creation.

2. To open a graph double-click on a graph file. A window will popup. You can create nodes using RMB, and connect those nodes. To delete a node select it and press delete key.

3. To save the graph click save button inside the graph window.