Luca,
If there's only two users, the fastest and easiest way will be to set a Thunderbird profile up with both the old mail folders and the new Scalix IMAP folders open, then cut'n'paste the contents manually.
If Thunderbird is running against an IMAP server currently (from their ISP or whoever external), then you can use IMAPSync (http://freshmeat.net/projects/imapsync/) to convert a bunch of mailboxes in the background, but - really - for two, I'd just roll my sleeves up and DIY.