The best thing to start is to try out all functionalities of Graph'O->Mat. If you already have installed Graph'O->Mat , then start it up, otherwise read section 4.1 on page 
first.
As you can see, you have to maximize the window to see the whole workspace. If this is not enough, try to set the screenresolution to 1024 x 768 pixels, which is fairly enough. Now, we generate a random graph by clicking on the menu 'Modify' - 'Generate Graph'. You can see, that your workspace is more or less filled with a random graph. If you want to get a bigger graph just click on 'Modify' - 'Modify - More' or for a smaller graph on 'Modify - Less'. This randomly adds or deletes some vertices and edges. For modifying randomly (you don't know if your graph contains more or less vertices) you can use 'Modify Randomly'. To change the layout of your graph randomly, you can use 'Shuffle Graph' which distrbutes the vertices new on the workspace, but lets your graph unchanged. Now, knowing how to change a graph randomly we want to change the graph to suit our needs. To move a vertex, you have to change to the move mode (see statusbar if you're already in that mode). Click on 'Vertex' - 'Move Vertex' to move vertices around. To move several vertices simultanously, you have to select some vertices and then to move this selection. First, go to 'Select' - 'Select/Deselect Vertex'. In the select mode you can click on a vertex and you can see that he changes his colors (inverted). To deselect a vertex, just click again on that particular vertex. Now, if you have to selected some vertices, change to the 'Move Vertex' mode in the menu 'Vertex' and drag a selected vertex. You can see that all other vertices which are selected follow your mouse. Now, we deselect all vertices by choosing 'Select' - 'Clear Selection'.
Until now, you can move and randomly generate and modify our graph. Now we go on and add and delete vertices and edges to a existing graph or even create a whole new one. First of all, we delete some vertices of our generated graph. Use 'Add/Delete Vertex' from the menu 'Vertex' and click on an existing vertex to delete him and all his connections. By clicking on the empty workspace you can create a new vertex with the lowest unused number. To remove edges choose 'Delete Edge' from the menu 'Edge' and click on two connected vertices sequentially. To add an edge just use the menu entry 'Add Edge' and click on two unconnected vertices. To create whole new graph, use 'New' from the menu 'File' and confirm the destroying of the former graph. Now select 'Add Vertex', 'Add Edge' and 'Move Vertex' to create your own graph. If you want to save your newly created graph, just click on 'Save' in the file menu and enter the path where you want to save your graph and a name. To load a formerly saved graph (or one of the example graphs of this distribution) you can select 'Load' in the file menu and enter path and filename.
By now, you are able to modify and create graphs by our needs. The only thing left is the intelligent placing of the graph. But you have not to do all the placing all alone. Select 'Standard' from the menu 'Optimize' and you can see, that your graph automatically tries to get a better layout with lesser crossings and smaller edges. Just try the different algorithms in the optimize menu and convince yourself of the power of these algorithms. You can find a more precise explanation of the different algorithms on page .