Implementing Active Directory with two controllers, four sites, total of about 150 computers

We are a small company still running on a NT 4.0 SP4 Domain.  We just bought a IBM rack mount, installed Win 2003 Std Server SP2.  Our company has a headquarters of about 125 computers and four small remote locations with a total of about 20 computers.  Two of them are tied to our cloud and the other two are on VPN's.

I've set up the DC, ran dcpromo and have my "root".  I'm getting lost on creating links for the sites that have different subnets.  Anybody have any design and/or implementation help?  We wanted to create a whole new domain to start from scratch since our network is small and not complex.  If it'd be easy to "upgrade" or migrate the NT 4.0 Domain, and then divide it into the sites, I'd consider it.

There is another 2003 box that will be the backup or secondary Domain controller but haven't done anything to it yet.

Thanks.