As of Oracle SQL Developer Data Modeler (SDDM) version 3.1.00.700 you cannot use external tables in Relational Models. When you import external tables from the Oracle data dictionary into SDDM you get the external tables in the Physical Model, but you cannot use them in a Relational Model.
I have figured out a work around until this is supported in SDDM. In SDDM create a view which SELECTs each column from the external table. You can then use the view in Relational Models. You can name the view in SDDM the same as the external table or differently. In my scenario I created the view with the same name as the external table and will not create the view in the database. I am just creating the view in SDDM to represent the external table in relation models.