You want to create a connection object to manually set up replication between two sites.
Open the Active Directory Sites and Services snap-in.
In the left pane, expand Sites, expand the site that contains the connection object you want to check, expand the Servers container, and expand the server for which you want to create the connection object.
Right-click on the NTDS Settings object and select Create New Active Directory Connection.
Select the replication partner and click OK.
Enter the name for the connection and click OK.
> repadmin /add <PartitionDN> <DC1DNSName> <DC2DNSName>
Hopefully you will not need to create connection objects manually. Creating and maintaining connection objects is the job of the KCC. It can be a lot of work to keep your connection objects up to date by yourself, especially if you have a large topology. The KCC uses complex algorithms to determine the best partners for a domain controller to replicate with. The Windows 2000 KCC had problems generating very large topologies, but the Windows Server 2003 version is significantly better.
It is sometimes necessary to create connections manually if you find a replication problem and need to get replication going again between one or more sites. By creating a connection and forcing replication to occur over that connection, you can get servers back in sync quickly.
Recipe 11.23 for listing the connections for a server