I did this migration over a year ago.
You need to upgrade to a Windows 2000 Domain first because Exchange 2000 needs Active Directory. Actually there is a little more to it than that

you have to extend the functionality of AD by running a utility called Domain Prep.
I think by memory this is part of the set up process.
Also you need to make sure that you have a working DNS server (Required for Windows 2000 Active Directory anyway)
I had a nightmare installing Exchange 2000, the upgrade to Windows 2000 was easy (almost too easy) The only part was the Domain name, you have to have a FQDN for Windows 2000.
After reading lots of articles I am still not sure what the best answer on this is. My domain was called fred but we have a head office in Canada that uses fred.com, we were supposed to be intergrating with them at some point in the future! so I decided to call my domain fred.com (Bad move!). This was no trouble accept when I tried to access the corporate web site!!
(not the real name) it tried to resolve to a local machine!!
I had to fudge an entry in my DNS to cover that problem.
I also had to fudge something for the custom receipients that had @fred.com email addresses! I have just done a quick search and the common answer seems to be to use .local so I should have used fred.local!. Be warned though I read that there is no way to change the FQDN without a full re-install of Windows 2000. (I won't be doing that in a hurry!)
I had a spare server so I installed Exchange 2000 and ran domain prep etc etc, the set up takes ages. When I tried to get the Outlook clients to connect they couldn't!! I am not sure how I fixed it in the end, I just tried installing it again and again, I think it worked on the 3rd or 4th attempt. I think the domain prep process is critical to the succesful installation of Exchange 2000, also the DNS server must be functioning correctly.
Once you have Exchange 2000 running and coexisting with your Exchange 5.5 there is an Active Directory connector you can use to migrate across the email accounts etc.
All this is from my memory of doing it over a year ago, hopefully those with more than one migration under their belt could give you more tips!! or correct me if I have made any errors.
Also there are some good books on Exchange 2000, I would say they would be money worth spent when trying a task like this.