In brief: To remove a reference, click on the remove reference button on the node's menu. To establish a reference, right-click on the node where the reference should originate and drag it close to the target node. Releas the right-click to establishes the reference.

Use the delink option on the menu to remove a reference.

In case multiple nodes would accept the reference, the one closer to the node where the reference originates will have its ring highlighted.

Once established, the reference is visually represented by a faint grey dotted line. Such line is visible only when both ends of the reference are visible and when hovering the mouse over the node.