I am running UBUNTU. Linux and have tried BOUML, which can show the project in a tree structure, but I am unable to get a diagrammatical over view of the whole system.
I think this is not a direct programming question, but hopefully it can be answered here anyway. :)
Also, would appreciate a good place to start to learn more about UML as it is becoming increasingly important in my project management.
I am not sure what format you have at hand, but I assume, you have XMI and that format does not contain any diagram specific information, it is only about the model, which is represented usually using tree structure, because it is the easiest way. For a diagram you would need to visualize the model and most importantly use some sort of layout algorithm. Layout for large models is quite hard especially with many associations and automatic layout might produce diagrams, which are misleading.
There are many books and places where to start with UML. I would recommend a book, e.g. one from Martin Fowler or Ila Neustadt and Jim Arlow. Recently modeling languages portal released list of UML cheatsheets.