How to subscribe to particular IMAP folders in Mac Mail
I had this same issue. I am using Mail version 8.2.

I found this to be a fix for me.

When I create a new account in Mac Mail, it shows the account name under "Inbox."

Under that account name are four folders - Sent, Drafts, Junk, and Trash.

You have to click on one folder at a time to highlight it, then in the top menu, select Mailbox > Use This Mailbox As > and select the correct mailbox (Sent, Drafts, Junk, or Trash).

When I did this, my Sent, Trash, Junk, and Draft folders that were under my email account name, moved under the "Main" Sent, Trash, Junk, and Draft sections. It took a second or two for them to sync to the server and not show a warning sign next to the folder name.

Under Mail > Preferences > Accounts > Advanced, I left the IMAP Path Prefix blank. I did change the Port from 143 to 993, checked the Use SSL box, and set the Authentication to Password. I used these settings because they match what my host provider provided me to use for my Incoming Server settings. I'm not sure this mattered or not.