The Employee checkbox is available in an Individual Relationship record. It indicates whether that individual is an employee of the organization.
The Employee checkbox indicates whether that individual is an employee of the organization. An individual may, for example, be a contact for that organization, but not an employee, or vice versa. For an individual to have that organization marked as their Primary Business Information on their constituent record, they must be marked as an employee of the organization. This field is useful in query and export. For example, you can query on organizations with relationships marked as employees, but not as contacts.