Transferred to new machine, trying to copy over "Mail" folder in Library

Have you also backed up your preference file?

Mail preferences and messages
Your Mail accounts, rules, signatures, and Smart Mailboxes preference settings can easily be backed up. Tip: All Mail-related preference files should be backed up or restored as a group.

To back up:
Note: These steps back up Mail preferences, but do not back up Mail messages (emails), although you can do that with the .Mac Backup utility. See below if you want to manually back up Mail messages (mailboxes).

Create a uniquely-named folder on your desktop (or other favorite location). For example, you might call it "Mail Prefs Backups May_15_2005" (adding a date is a good idea).
Quit Mail if it's running.
In the Finder choose Home from the Go menu.
Open the Library folder.
Open the Preferences folder.
Copy the "com.apple.mail.plist" file to the folder you made in step 1 by Option-dragging the file. Don't remove the original file from its current location (this file contains your Mail accounts information).
Close the Preferences folder.
Open the Mail folder.
Copy the "MessageRules.plist" file to the folder you made in step 1 by Option-dragging the file (this file contains your Mail rules).
Copy the "SmartMailboxes.plist" file to the folder you made in step 1 by Option-dragging the file (you guessed it, this file contains Smart Mailboxes information).
Finally, copy the Signatures folder to the folder you made in step 1 by Option-dragging the folder. (Your custom signatures, if you use them, are stored here.)
To restore:
Move all copies of the files and folders from your uniquely-named folder to the original locations from which they came, as listed above.

To manually back up Mail messages (emails)

You might wish to manually back up all your Mail messages from time-to-time. To back up entire mailboxes (where Mail stores messages), such as your Inbox, follow these steps:

Quit Mail if it's open.
From the Finder's Go menu, choose Home.
Open the Library folder.
Copy the folder "Mail" to your backup location, such as a different volume or burnable disc. Important: Do not remove the Mail folder from ~/Library. If you're backing up to the same volume, hold the Option key as you drag the folder to make a copy instead of moving it (a "+" cursor appears).
You can restore backed-up mailboxes at any time by quitting Mail and following the above steps, except for the last step where you copy your backed up Mail folder to ~/Library, instead of from it.

from http://support.apple.com/kb/ht2980#mail

How do point Mail to the data I want it to see?

Hi there!

OK so last week my hard drive start acting weird (locking up, crashing, etc) so I promptly backed up using Time Machine, which I do every day anyway, and then took my Macbook Pro to my local repair shop where they installed a new hard drive and imaged all my old data onto the new drive. I have my Macbook back and everything looks perfect (all my applications are exactly where I left them, all data is still there, etc) EXCEPT when I go to open up Mail it says "Welcome to Mail" and acts like its being setup for the 1st time. I have all the mail data and can see where it is in my Library folder so how do I get Mail to "pont to it" or recognize it. I'm scared to re-setup Mail before I figure this out because I don't want Mail to setup a whole new mail folder because I won't know what's what.

Help!!

--Jeremy

Have you taken a look at the Preferences folder on your new HDD and on the Tine Machine HDD and seen if they are the same?

Have you read the above post?