Peter,
Have you tried using the primary key prefix to specify the existing fields to "Update" instead of "Add"?
Example spreadsheet...
Headers:
PK:External ID | FirstName | LastName | Email ....and so on.
This should find the data and allow you to do an Update instead of Add. There are tips in the documentation as well....
http://usermanual.clarizen.com/#16-5-data-loader