Trusting Windows NT and 2000 domains

I am currently in the middle of an upgrade to Windows 2000 from NT and I am having trouble with a trust between the two. My NT network did not have DNS and functioned on NetBios and WINS along with a VPN to differently named domain (which has a trust established). Essentially what I want to do is bring all NT domains into one (site.local) and be able to have users access programs and data regardless of what domain they are joined to.