Automap matches the fields from the Available Fields with the fields in the Target Data Extension based on names and field types.
There are two scenarios where Automap will not work:
1) The field type is not compatible.
For example: An Email field isActive will not match to a Boolean field with the same name.
2) There are multiple fields under Available Fields with the same name.
For example: If you have joined Accounts and Contacts Data Extensions and both have an Id field, Automap will not map to an Id field in your Target Data Extension.
Recommandation: Use Automap to get the majority of your fields mapped, and then map the remaining ones manually.
(Do Not) Overwrite
Automap has 2 options: Overwrite / Do Not Overwrite
When Overwrite is chosen, any existing mappings will be overwritten by the mappings defined by the Automap functionality.
When Do Not Overwrite is chosen, automap will try to map fields that were not mapped yet, but will respect any existing mappings.