IMAP Mail Synchronisation

I'm using IMAP in the Mail application on my iMac and on my iPad. Both work fine but there seems to be a problem with syncing of messages between what's held in the mailbox subfolders on my desktop computer and what's on the server.
For example, if I send a message to myself on the iPad and then move it into a subfolder on the iPad the message appears correctly in that folder on both the iPad and in the 'server' section of Mail, which is called 'RAY'S MAIL'. However, the message doesn’t appear in the corresponding 'ON MY MAC' folder, no matter what I do. Rebuilding the mailbox, asking Mail to synchronise, restarting the Mail application: nothing fixes it.
Similarly, if I send a message to myself on the iMac and move it to the folder in 'ON MY MAC' and then try to sync the folders it doesn’t put it into 'RAY'S MAIL'. Now I confess that I originally dragged my folders from 'ON MY MAC' onto 'RAY'S MAIL' to create them in the first place, simply because selecting 'Synchronise' didn't create the folders. I thought it was all working fine, as most items actually appeared to be syncing, but this clearly isn’t true for much of the time.
This is all horribly boring and tedious, but if anyone has any good ideas about fixing this I'd very much appreciate them.
Many thanks,
Ray

OK, I threw away the 'Mailboxes' folder in Mail's folder in the 'Library' folder and restarted Mail. I now only have 'RAY'S MAIL' the sidebar of Mail that I'll work with. I note that the server data is also stored on my computer at Library/Mail/V2/ in my account name, so this appears to be the solution, but please correct me if I'm wrong!

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