In some situations, such as when your network is not fully routed, you may need to manually create site link bridges in order for replication to have a path to follow. If this were the case, you could turn off the automatic bridging of all site links and define the bridges that you wish to exist in AD Sites and Services. Note that site link bridges do not need to be created in a fully routed network, since all site links are bridged by default, allowing the lowest cost replication path to be calculated automatically. You should also note that Active Directory does not control the Layer 3 routing of data – site links allow replication between sites, and controls which sites are connected for the purpose of replication. The actual path that the data will follow over the physical network depends on how routing has been configured in your environment.
You should also be aware of the replication troubleshooting tools that exist. The two main tools are Replication Monitor (Replmon.exe) and Repadmin.exe. Replication Monitor is installed along with other advanced tools from the Support\Tools directory on the Advanced Server CD, and provides a great deal of information about the replication environment including the ability to view USNs, view replication partners, view replication status on a server, trigger replication between partners, and so forth. Repadmin is a useful command-line tool, but provides information about only a single domain controller at a time.