Place the jar file in your server plugins directory.
Start a REPL
Run this from your server console:
/repl start [port]
The default port, if left unspecified, is 7071.
Stop the REPL
The plugin will remember whatever state you left the repl in (running or stopped). If it was running when the server was stopped, it will be started again when the Bukkit server starts. By default, the REPL is disabled until you start it.
See config.yml in your plugins directory. There you can change the port and even the host/IP where the REPL server will listen.
Building your own Clojure Plugin
For details on how to build your plugin using the Clojure language, see the Bukkit4Clojure GitHub project page.