Hmmm... In Thunderbird I used to keep my old emails organized in subfolders -- if I copy all the messages in a subfolder and paste them into the Inbox, they're there but I don't see a way to keep them in a subfolder. Whenever I try to create a new mailbox or smart mailbox folder (the only folder option I see), it isn't created as a subfolder of Inbox, but is added to the "On my Mac" section where all the imported mailboxes already are.
In other words, there seems to be a universal unalterable inbox, sent, junk, etc mailbox (showing at the top left of the mail sidebar), and any other mailboxes I create are put into the separate "On my Mac" section.
And even though there's ostensibly a "Use this mailbox for..." option, on every mailbox I look at, all the options are grayed out.
And I don't see anything in the preferences to allow me to set which mailbox to use for inbox, sent, etc.