JIRA/Greenhopper are highly customizable. In order to achieve a consistent usage across different projects and users, the following guidelines should be followed using the issue tracker.
Backlog management
Currently, Greenhopper offers three types of issues: Bugs, features/user stories and tasks. We use them in the following way:
- Bug: This issue type is self-explanatory. Use it for bugs which occurred outside the current iteration.
- Feature/Story: This issue type is used for user stories. A relative estimate (story points) can be assigned to them. A user story normally consists of multiple tasks which are derived during sprint planning. Create these tasks as sub tasks of this story, not by the issue type "task" (see next bullet). A sub-tasks can easily be created using the green mini button on the story card:

Normally, you won't assign a duration estimate to a whole story – the duration is calculated automatically by the sum of all sub-task durations. Instead, we use the relative story point value, which is shown in the lower-right corner of the card.
- Task: This issue type is reserved for other tasks which are not related to product-owner-driven stories. Examples are organizational tasks, resolvement of road blocks etc.
Working with the task board
A good idea is to use the drag n' drop feature in Greenhopper task board. Simply drag your card from the TODO colummn to the IN PROGRESS column when you start working on an issue and drag it to the DONE column if you have it resolved. This is not only faster than editing the issue the classic JIRA way, it also reminds you to set the remaining estimate to 0, when resolving the issue.

Releases and Iterations
Releases and iterations are managed in JIRA/Greenhopper by so-called versions.
You can manage versions e.g. by clicking on "Manage" link in the right column in the planning board view of greenhopper:

Both releases and iterations are created as a version. An iteration version is related to its release by assigning it another version (the release) as a master:

Estimation and Progress
As mentioned above we use three types of issues: Bugs, features/user stories and tasks
- Features/Story are estimated using the field story points and the burndown/burnup charts used are based on the number of resolved issues of this type or the story points. The effort spent is aggregated via the subtasks.
- Bug, Task, Subtasks are estimated using engineering hours. Please be so kind and use the log work function and log the remaining time and the time spend. The burndown charts used are based on remaining time (effort) and resolved issues.
Please keep in mind: The burndown on story points and remaining time are good for nothing if you don't estimate the issues and log the work as you work on the issues.
General documentation
The Greenhopper documentation explains the general usage of greenhopper.