I've got some good news. You don't have to duplicate what you have in your project management (PM) software. Everything in that software is support material. Here's what you really need to track in your GTD system:
Your project schedules, plans, gantt charts, etc. stay in your PM software as support material. Use them to track your progress and define your next actions, but don't double-enter these items in your GTD system unless you really feel the need. For example, you might put the deadline of a deliverable or milestone on your calendar as a day-specific reminder.
- The reminder of the project itself (Complete R12345 - VB to J2EE Migration of Online Product Inventory System).
- The very next physical action(s) that you need to take to move the project forward. Think of these as bookmarks, not "To-Dos". When you walk away from the project, these bookmarks will help you to kickstart progress when you return. (Example: Call project sponsor re: project scope)
Some extra tips on working with a project focus:
If you've committed to working on a specific project, record a new next action on a piece of paper each time you finish an existing next action. Cross it off if you complete it right away, define a new one and repeat. I've spent entire days doing this without ever touching my GTD lists after doing one next action from them.
When you need to walk away from the project, toss that piece of paper into your inbox. The next time you process the inbox, the action will get onto your lists. If you forget to do this (and you will in the heat of battle and switching gears), a regular review of your projects list (usually during the weekly review) is your safety net to prevent projects from becoming orphaned (stagnated due to no next actions defined for them).
Best of luck!