Microsoft Project is a great tool for creating task/schedule hierarchies for project tasks. It well-integrates with TFS. Whenever you run a query to import work items it'll automatically filter out duplicates from your WIQL results. It provides a grid of non-duplicate work items meeting the WIQL criteria with the first column of checkboxes pre-checked. This way you can further filter out work items to bring into your project plan document.
The problem is that all the new work items come in "at the bottom" of the MS Project plan. The solution can be found at http://office.microsoft.com/en-us/project/HA012111441033.aspx under the heading "Moving tasks". Here are the steps to follow:
1. Remember to drag and drop, and do not cut and paste.
2. For the task you wish to move, select the entire task row by clicking the gray row heading, which includes the task number.
3. Point to the row heading until a four-headed arrow appears, and then drag the task to where you want it in the active view.
4. A gray line along the row border indicates where the task will be inserted when you release the mouse button.