Hi
3D graphs unfortunately usually take up a huge amount of resources even for small maps since there are so many cells.
However if you want to go with this, the easiest way is to use a point graph and arrange a bunch of objects in a 3D grid. Also make sure that the maximum connection distance is just slightly larger than the distance between two objects in the grid.
You can also create a custom graph (see the documentation for a tutorial), but initially it will likely be a lot faster to start with a point graph.