Linux can get Windows domain accounts by using Samba - which you can use to join the Linux server to the domain and your users could access it like any other Windows file server:
www.samba.org
If you want to automatically use Windows usernames/passwords in other servers, if your FTP server supports PAM, you can use a Samba component called Winbind to do that. IMHO, there is a bit of a learning curve to do it. You could also possibly skip Samba, since Windows 2000 Active Directory uses LDAP and Kerberos, you may be able to directly authenticate using one of those protocols, I've never done it myself.