I don't know if I fully get your problem, but I think you could just create associations between your entities and set them by iterating over your imported entities and search the matching parent entity by key (do a db retrieve and only retrieve the object with this key).
You can first import the tables from Excel to the Mendix app.
After it is imported you can create a microflow to link the two entities together by using the two id's.
You can do this by retrieving the complete list of the first object in a microflow, then loop over this list and search for the other object that has the ID that is supposed to be linked to the iterator object (the object in the loop).
Once you've found it you can set the association.