You need to add these folders in your IMAP mail account.
If for example you are using Gmail login, and create the folders you want using the webmail settings panel.
When you next launch mail the folders will be there and you can then drag and drop emails into folders, etc.
Outlook doesnt create the folders in IMAP it creates them on the machine, so they are not true IMAP folders they are just folders in Outlook.
Chase reports and asks:
Also, the folder ~/Library/Mail only has two folders
Mail Lost+Found
V2
All of my mailboxes are contained within V2... is that normal?
Those folders should exist, but at least based on the contents of my own ~/Library/Mail
folder, it's incomplete. I also have individual folders for each of my email accounts and those folders contain mbox files which I assume are the local copies of the IMAP mailstore.
By way of troubleshooting, it might be interesting to know what the file permissions are for the Mail directory.
Open the terminal, and type (or cut and paste) the following command:
ls -l ~/Library/Mail
The results (edited here to show only the relevant line) for my own functional Mail folder are:
drwx------ 13 jaberg staff 442 Oct 13 00:25 Mail
The permissions basically tell us that this a directory and that the owner, jaberg (me) is able to read, write and execute. (The execute permission of a directory is sometimes thought of as the search permission. You need the x in order to be allowed access to the information about the contents of the directory.)
You can also view permissions from Finder by selecting the folder and performing Get Info… from the file menu (or ⌘+i), but you won't get as much information.
You'll find more information about accessing and interpreting file permissions in the Apple Knowledgebase: Troubleshooting permissions issues in Mac OS X
If you're permissions differ from those shown here, you can try to Repair Permissions using Disk Utility (this doesn't require a restart or booting from a different volume) or, if you're comfortable, change the permissions of the Mail folder to match those shown using the chmod
command. You can learn about chmod from its man(ual) pages, accessed from the terminal by typing:
man chmod
Best Answer
Steve Price's answer pointed me in the right direction. I'm running El Capitan, and found the .mboxCache.plist files under /Users/my login/Library/Mail/V3. The file is a text file, and can be edited with a text editor (after closing the mail program).
For folders appearing in the wrong place, the problematic entries are as follows:
The value "0" puts the folder at the beginning, higher values go later in the list.
If you simply remove the two above lines for any folder appearing in the wrong place, and restart Mail, those folders will go back to being sorted alphabetically.
Sometimes the following two lines also appear in combination with the above:
In those cases, I changed "true" to "false".
Now my folders are back where I want them, yay!