As far as I know, there is only one "INBOX" in IMAP server. (It's the same for POP3, and probably for EWS, ...)
In any case, - the notion which folder is "Inbox" is internal for the server, and you cannot change that, regardless of the name of other folders.
Also, just in case, - keep in mind that even though Aquamail will treat the folders you created (Sent, Deleted) as such, if you set the appropriate designation ("Sync as [sent]", "Sync as [deleted]"), but,
The server will not understand that. So, if you were to do something in Yahoo web interface (delete messages, send messages), - Yahoo server will save the sent and deleted messages in the respective "original" folders, not in those those you created for Aquamail under "root/".