Needs quick overview how to use discovery tool.
Product Manager for Notes Migrator did training where he explained all details about NMPS usage. There are 7 sessions. The Session 2 contains information about discovery:
http://communities.quest.com/docs/DOC-11151
Also, if you have any additional question, you can post them on Notes Migrator community:
http://communities.quest.com/community/sharepointforall/notes?view=discussions