GPS->Track->Clear will only the track that is currently being recorded, as you've noticed.
Recent versions of the product have two top level menus - Program and Action. See this page:
http://www.backcountrynavigator.com/content/view/101/46/If you haven't updated since December 2007, it will look different. Go to the list page, choose Tracks in the drop down menu, and push Load. You will find the lists of Tracks there to Edit or Delete.