You're up for a hefty upgrade if you're going to try integrating your existing ex5.5 site with your unity server. You've got a lot of things you're going to need to decide first:
1. Are you going to try integrating your ex5.5 stuff into your ex2k stuff, or vice versa?
2. Are the servers your ex5.5 sites are running on already a part of an AD domain? If yes, is it the same domain as your ex2k server?
There's a lot of things that are going to go into this move. If your ex5.5 servers are already a part of an AD domain, then to add the ex2k server means you'll have to reinstall ex2k. If the ex5.5 servers aren't in an AD domain, then you can simply add them as member servers. In either case, once everybody is in the same domain, you'll need to set up the ADC so your mailboxes can see each other regardless of their version of exchange. Once that groundwork is finished, getting Unity to use this new environment is a snap. Be sure to use the DiRT tool first to make a backup.
adam