Phone, iMac, Laptop sync question.

My iPhone, iMac, and Macbook (both running Yosemite) are all synched via the Cloud. I knew that when I deleted recently received mail messages on my phone, they would then be deleted (i.e. not download from the server) when I opened mail on my desktop computer (and vice versa). I recently discovered that old message that I want to keep (even in sub Mailboxes) on my desktop Mac, are being deleted if I delete them on my phone. I sometimes do this because I don't want to use up space on my phone, but some these messages are important to be archived, saved, on my desktop Mac.
So what is the process to be able to delete messages on my phone, but make sure they are saved on the desktop Mac if I have moved them to Mailboxes. Does it involve turning off Mail sync via the Cloud on the iMac? Or "archiving" the messages I want to save on the iMac?
Thanks for any advice.

Save them to an 'On My Mac' folder.

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