MineOS is pre-configured to work with bukkit. The server jar is downloaded by default and can be selected simply from the drop-down when creating a new server. That's all you need to do to get a bukkit server up and running!
Managing the server
Substituting minecraft_server.jar (official vanilla release) with craftbukkit-0.0.1-SNAPSHOT.jar is completely transparent, which means that you can use the web-ui the same way for any given mod, such as starting and stopping the server.
Bukkit on its own is only marginally different from vanilla Minecraft. However, with the huge number of user-contributed plugins, bukkit quickly and easily allows you to modify nearly every aspect of your Minecraft server.
When you download plugins, the must be placed in the 'plugins' directory of your server. In MineOS CRUX, this can be located at /home/mc/servers/<servername>/plugins. The easiest way to move them onto your server is using a file transfer program like Filezilla or WinSCP, using the SFTP protocol.
At any given time, the bukkit dev team has one build designated the 'recommended' build. However, as an admin, you may wish to hold onto an older build to maintain plugin-compatibility for the time being or to try a newer build to test if plugins break. To use non-recommended builds, the prescribed way is to upload the jar to the /usr/games/minecraft directory with a unique name, such as bukkit-1374.jar.
In the web-ui, the server will detect all .jar files and list them directly in the dropdown box. Rather than replacing the existing craftbukkit jar, using this method will allow you to quickly switch between the two (or more) server jars.