Mozilla Thunderbird version 1.5 stores all your settings, emails and other stuff in ~/ .mozilla-thunderbird/ directory.
Mozilla thunderbird version 2.0 stores all settings in ~/.thunderbird/ directory. So when you download and upgrade your version you will get a blank and new mail client.
To get back your mail and other settings all you have to do is copy everything from ~/ .mozilla-thunderbird/ to ~/.thunderbird/ directory.
#1: Shutdown thunderbird
#2: Open a shell prompt / X terminal and enter:
$ cd .thunderbird
$ cp -avr ~/.mozilla-thunderbird/* .
#3 Start thunderbird and it will import everything including mails and other settings :)
#4 Don’t forget to update your extensions for a new version ;)