Not sure how it was still there if you don't know how to put it there. As far as I could determine, it isn't enabled by default.
Hover your cursor over the Favorites header in the Mailbox list. On the right side you should see a + button. Click that and add the "All whatever" mailboxes you want, and any other "favorite" mailboxes.
You can also ctrl-click on any Mailbox and add it to Favorites.
Also note that adding to favorites does not remove it from display under the account. There is nothing wrong if you still see the Inbox under the account header.