To create new nodes, drag nodes from the blue circle in the lower left corner onto the stage.

To remove nodes, drag them from the stage into the black circle in the lower left corner.

Nodes can be dragged around the stage at any time.

About the Algorithm
Here's what I was trying to accomplish with this algorithm:

The "Arrage2" button uses the better algorithm. Equidistant positions are calculated for the number of nodes on the screen. The nearest node that is within a certain distance of a position will be assigned there. For any remaining nodes, if one its two nearest positions are unfilled, it will occupy that position. Otherwise, it will kick out the node in one of those two nearest positions, and the displaced node will displace its neighbour and so on until an empty space is found and filled.