Use the child entity as the Mendix object for import.
In the column(s) where you need to import to the main (parent entity), use following settings in column details :
Type - Reference
Reference - The association between parent and child
Object type - The parent entity
Attribute - The attribute you want to import the column data into
Make sure you have atleast one column from the main entity to be unique and can be used as key. You can do this by choosing Key - Yes, only for associated object. This would prevent duplicates in the main entity to be created on import.