Theres not really an easy answer. Depending on the size of your domains the planning process for deploying Windows 2000 could take quite a while. The easy (but not the safe way) would be to start with one domain, upgrade the PDC and you got that domain changed to a mixed mode Windows 2000 domain. The trust relationship to your other domain is still there so everything works fine. Now you can upgrade all the DCs in that first domain, then the member servers and workstations (even though this is not necessary). You will go through the same process for the other domain - this time make sure when you run the upgrade that you join an existing AD forest (the one you created when you upgraded the first domain).
There are plenty of things that could go wrong - you might want to read a little more before deploying - especially DNS, your site structure and replication topology, fsmo role placement is worth knowing before you start deploying.