How to import .eml files into Mail?
If you put the exported e-mails (*.eml files) into a folder structure, then just select the outer folder as the import folder.

The test import I just did is like below:


Select "Apple Mail" as the "Import data from":


 


Select the outer (root) folder of the e-mails to import:





Confirm the selection: 





The imported .eml e-mails is now in an 'import' mailbox (only one mailbox) with the same folder structure as the folder the import came from:




Now you can move all or selected e-mails from the import folder to the mailbox of choice. When all e-mails has been moved, just delete the 'import' mailbox.