It sounds like you're asking if you can "seamlessly" migrate computer and user accounts from a Samba domain into an Active Directory domain.
Current "stable" versions of Samba don't emulate an Active Directory domain, but rather act like a Windows NT 4.0 domain. You won't be able to just "upgrade" the Samba domain to Active Directory (although I'm getting a perverse desire to put up a Samba domain, join an NT 4.0 BDC to it, promote the NT 4.0 BDC to a PDC, remove the Samba BDC, and upgrade the Windows NT 4.0 machine to Windows Server 2003 just to see what would happen).
Your best bet, since you want to build the Windows Server 2003 Active Directory domain in parallel to the existing Samba domain, anyway, is to use the Active Directory Migration tool (ADMT). From what I'm reading ADMT works with Samba and the process appears to be reasonably painless (it looks just like ADMT'ing from an NT 4.0 domain, to my eyes). I haven't done it myself, but it looks worth trying. At the least, you could spin up a test Samba domain, join a couple of test PCs to it, and do a test migration before running on the production domain.
It can still be pretty seamless for the users, though. You can setup a trust relationship between the existing Samba domain and the new Active Directory domain and then migrate computer and user accounts at your own pace.