The import/export tool will take care of getting all the mailboxes created on the new system and getting your subscriber data in as you've figured out... for moving the messages you'll want to look at using ExMerge. Since the aliases (UIDs) between the old system and the new system will match, ExMerge is ideal since it uses the aliases to match things up as well.
check out the "migrating unity" doc on AnswerMonkey.net here:
http://www.answermonkey.net/General_tools.htm
it has some instructions on how to use Exmerge if you're not familiar with it.