Like other areas of Importacular, the Education Area Settings (to learn more about the difference between an Area Setting and a Field Setting, click here) allow you to avoid duplicate Education Relationships.
The one notable difference between the functionality in this area is that you do have to set some criteria in order for the Education Relationship to be matched to data in Raiser's Edge. In other areas, there are some defaults (such as an Attribute will always match on the Attribute Category), but in the Education Area Settings, you have to determine what to match on (though the system defaults to the Establishment/School Name and the Is Primary checkbox).