Hi Claudia,
The force directed layout plugin auto-layouts graphs based on three forces: repulsive force (forces nodes to move out of each other), attractive force (tries to get nodes together like a spring) and a gravity force (tendency of the nodes to move to a certain point).
The gravityCenter parameter is the point the nodes tend to move to. This is usually set to the center of the area where the nodes are to be layouted.
charge parameter affects the repulsive force. Bigger the parameter is, bigger the repulsive force.
linkDistance and linkStrength both affect the attractive force (you can think of it as parameters of a spring that tights together two nodes). Bigger the linkStrength, bigger the attractive force between two connected nodes. On the other hand, smaller the linkDistance, shorter links you allow and so the attractive force is bigger between two connected nodes.
There is no one-fits-all set of parameters that would give great result for all possible graphs. Therefore, I suggest you to play with parameters, try to set different values so that it gives a good result for you use case.
The other related issues is hard to answer without seeing a code snippet on how you use the plugin.