Uploader can be used for large imports however it has a few failings such as I have never worked out how to upload privileges. However to answer your question as far as I have tested it will not overwrite information but will update fields that are blank for currently existing users. Apparently you can deactivate users but I have only ever used it on fresh installs to do an initial upload. It will not create duplicates, as far as I have tested it will keep current entries but update missing fields.
Following is the list of coloums for user import. If creating your upload using excel you must have a space in the last column to ensure all commas exist otherwise the upload will not upload correctly:
First Name,Last Name,,Nice login,Nice password,Pin number login,A,,,,,,,Department,Location,,,Pin number login,1,,,,
Obviously I have ignored some fields which I never use, the A is for Active user, the 1 after pin number login is for Site 1, set all users with these values if they are new users and you only have one switch instance. I always add the same value to the two pin number login fields, this is supposed to be either extension number in a fixed seating environment or agent id in a free seating environment but how you have configured your CLS as fixed or free seating is which of these fields the importer will use.
To import department and location type fields you must first run the import once, to load the base agent details and then run the import again to add these details to the agents (note that the import will automatically add any departments or locations that are in the import but not currently in your CLS lists). Don't forget to rename the import file between imports.
If importing Members/Leaders first import users and then run a second import for the members / leaders.
I have never tried importing workflow management stuff.
Most importantly test your import file on a test database before trying it on a production system as any errors will cause incorrect fields to be populated.
Good luck
Good luc