This is tricky, but I just figured it out. I'm surprised Apple doesn't have good documentation on this. The trick lies in TWO things - migrating both your Apple Mail Items AND the Internet Account Items. Before Yosemite, your email accounts were all contained in the Apple Mail folders. However, now they have been separated so if you JUST manually migrate the Apple Mail stuff, without the Internet Accounts, then Mail will open and you'll just get your a nakedn iCloud Inbox that will start to load your most recent emails. Also, it helps to copy the Keychain folder over so you don't have to re-enter all your passwords (in Mail or other places as well).
These are the files you need to copy over from your user's Library folder:
for Internet Accounts
.../Accounts (folder)
for Mail
.../Mail (folder)
.../Mail Downloads (folder)
.../Containers/com.apple.mail (folder)
.../Preferences/com.apple.accounts.plist (file)
.../Preferences/com.apple.accountsd.plist (file)
.../Preferences/com.apple.mail-shared.plist (file)
.../Preferences/com.apple.MailMigratorService.plist (file)
.../SyncedPreferences/com.apple.mail-com.apple.mail.vipsenders.plist (file)
.../SyncedPreferences/com.apple.mail.plist (file)
for Keychain
.../Keychains (folder)
I arrived at this with a fair amount of trial and error. I had backed up my old user folder (all the folders, including the Library folder) with both Time Machine and a manual copy. I played around with these on a separate, dummy user account (so I could delete it and have my nice, pristine, clean install still there once I figured it out). Finally, let me also say - BAD on you Apple for making this so complicated. Email software is one of those things that should remain elegant, even at the architecture level. Quit complicating things.