advice needed in moving to new 2003 in a forest

In our school district, they did not set up the forest properly and thus all the domains (schools) show as being parallel to the forest rather than beneath it. I am now in the process of going to 2003 server in my school. I want to setup the new 2003 server correctly in the existing forest but I still then need to migrate all my AD etc from the current domain into the new one. Any suggestions on how to best approach this? Is there a method for curing this forest structural problem for the whole district that I might be missing?
Thanks in advance