If you are thinking that site links might be problematic, you might be right. For example, imagine if you were to create a new user account and the originating update were to take place on a domain controller in Toronto at 9am. If the schedule on the site link between Toronto and Vancouver only allowed replication between 6pm and 8am, the user account would not appear on domain controllers in Vancouver until after 6pm that evening. Note that this problem is easily circumvented – when creating the account in AD Users and Computers, simply connect to a different domain controller (say one in Vancouver) and create the account. This will make the originating update take place in Vancouver, and then user (presumably in Vancouver) would be able to log on immediately.
Connection objects between domain controllers differ within and between sites. Within a site, domain controllers will have many connection objects with other domain controllers. However, replication between sites happens via connection objects between domain controllers in each site that are designated as bridgeheads. Bridgehead servers are chosen automatically, but you can set a list of preferred bridgehead servers. The process that chooses bridgehead servers is the Intersite Topology Generator (ISTG), which runs automatically and will designate a new bridgehead should the current one not be available.
Another important consideration when setting up site links is the protocol that the site link will use. Active Directory supports site links via RPC (referred to as IP in the interface) as well as SMTP. Within a site, domain controllers use RPC. You should note that you would most often use RPC, since SMTP does not support replicating the domain partition between domain controllers in the same domain (this is mainly because the Sysvol folder is replicated using FRS, which uses RPC only). SMTP does however support replication of the Schema, Configuration, and Global Catalog partitions. SMTP is useful for distributed environments with unreliable WAN links.
By default, all site links that you create are bridged (transitive). What that means is that in calculating the best path for replication, all site links are considered.
For example, in the diagram above, replication between sites A and D would occur over the least cost path, which would be over the bridge automatically created – ABD, which has a cost of 20. Note that the alternative AD has a cost of 200, and bridge ACD has a cost of 110. In looking at all available site links, AB and BD were bridged to form the lowest cost path available. Site links are created in AD Sites and Services. As a best practice, you might consider naming site links after the sites that they connect.