Replication Agent uses TCP/IP and the Sybase JDBC driver (jConnect for JDBC, which is included in Replication Agent installation) to communicate with other Sybase servers. The Replication Agent does not rely on the Sybase interfaces file for connectivity information.
You can find a description of the Replication Agent configuration parameters that must be set to allow Replication Agent to connect to the primary Replication Server in Replication Agent Installation Guide > Preparing for Installation.