We've started using Jira and Confluence as a replacement for Xplanner (which we used for almost 2 years). Jira's an extremely flexible issue-tracking software product which allows us to track Bugs, Projects, Sprints, and even Ticket queues (like internal email support) all in one place. We hope to be able to relate issues to one another and discover trends, bugs, and manage our software process more holistically.

The challenge has been defining the mapping between Jira's entities and our business entities, mainly for managing the work in a given software sprint.

We've tried the following
Sprint: Version
Weekly Milestones: Due date
Category of change: Component
Type of task: Issue type
High-level task: Issue
Individual action in pursuit of high-level task: Sub-issue

This sprint we're trying something different:
Sprint: Project
Weekly milestones: version
High-level task: component
Type of task: description
Individual action...: Issue

Both have their pros and cons, what I'd love to know is how others solve this and whether they might have any advice on how they've configured the entities in Jira, use Links, etc to manage their Agile development projects.