I'm gephi main dev. That will be fixed with better documentation asap. You can add nodes and edges by using "Node Pencil" and "Edge Pencil" tools in the toolbar.
The coordinate system is obtained from a force-directed algorithm. Iteratively linked nodes attract each others, whereas non-linked repulse.
And to search, go to the "Data Laboratory" and filter. Right-click on a row and "Select on graph". Then go back to the graph, the camera is centered on the node.
It was in pre-release for a few weeks to address any regressions.