Removing duplicates, or "de-duping" is a simple process in EndNote. After you've imported all your references...
On the menu bar, select References -> Find Duplicates.
A dialog box will appear resembling this:
This box will display any duplicate records, it is up to you to confirm which one to keep, and which to discard. Click the Keep This Record button for the one you wish to keep. The other reference will be deleted from your library.
The box will reappear until all duplicate records have been handled.