Katie,
Only stages that have the category of "Open" will appear in the pipeline. Selecting stages with a category of "Closed Won" vs. "Closed Lost" really only affect reports you wish to generate down the road. For example, if you wanted to run a report for all the opportunities you lost in 2011.
You'll see over the coming months that we'll be releasing reports that leverage this data. However the graphs focus only on stages that have "Open" as the category.