How to relate departments and employees
How to relate departments and employees according to a common attribute using the connect-it automatic download of data if they are stored in the same table in amEmpDept?
You may need to supply screenshots and/or explain more, however, treat the root table in mapping as the employee and use the 'Department (Parent)' link branch for said department. Setting the reconciliation key(s) (ie. red keys) for both will give you what you want. These reconciliation keys do not have to be the same for each, however, they must uniquely identify a table record respectively.
When I wrote you may need to explain more, it is because I do not understand "...using the connect-it automatic download of data...". Does this relate with out of the box scenarios?