Understanding mail "On My Mac" and "iCloud"

Since the arrival of iCloud, I'm having problems understanding my mail.app mailboxes.
Sometimes I send mail from my phone and it ends up in one mailbox, then I reply on my computer and it ends up in a different mailbox. I don't understand the "On My Mac" and "iCloud" mailboxes. Of course, I know the difference between on my Mac and in the cloud, but why isn't everything the same in all the boxes?
At first, I thought, well, I don't want mail "On My Mac," but then I wouldn't be able to access it if offline. All I want is for my mailboxes to have the same stuff everywhere and not have all these different mailboxes. What am I doing wrong? Am I just not understanding how this works?
Any help would be appreciated. I'm using the latest versions of everything.
These are the screenshots of my email on my laptop and on my phone.

I did goto Preference > iCloud > deselect Contacts. It will ask to delete all contacts "on my mac" and accept it. After a while, I went to Contacts app and manually deleted the rest of entries. I also checked the Contacts on iCloud.com. So the source of Contacts on iCloud.com was only one.
Then I went back to Preference > iCloud > select Contacts and accept "merge". A few minutes later, my Contacts app on my mac are sync with the Contacts on iCloud.com.
I don't have "on my mac" or "iCloud" in my Mac Contacts app. 

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