Greenhopper is a pure agile process tool, with the main focus on planning for the sprints, ordering the backlog and tracking the work using the computerized agile boards. We've been trying to use it as a project tracking tool, but it's not really suitable for that.
Also we've been using Jira plugin called Structure to do the work which is more or less similar to the project management - it allows to create overarching items, subitems, tracks process and helps to do a lot of things that are relevant for the status communication part. On splitting up the user stories and creating subtasks etc. I would assume that your problem is creating a view how they are linked together, this is where Structure does help, as it allows the n depth tree structure to be created.
And after spending almost 4 years trying to figure out ways how to make things work, so that the needs of a project manager are satisfied and also the teams and it doesn't deviate too far away from the scrum - conclusion is that neither of them are perfect. Structure messes up the planning process as you have items in a tree and they don't easily correspond to sprints. And Greenhopper does not really let you do meaningful project management, as it does not show the relation between issues.
Atlassian, if I'm not mistaken, has recently launched a really neat tool, called Rapid Boards, which actually combines aspects of these quite nicely, so this is one of the things I recommend to take a look into.
P.S. I am more and more also inclining towards the opinion that post-it (tm) based agile board is really the most suitable thing for planning and paper and pencil are one of the most important tools for a project manager :).