Just go into your FTP and replace the server JAR with the new one from http://www.dl.bukkit.org and no offense but its kind of sad for me to see people relying on this because it is much better to do it through the bukkit website. I do this because Multicraft will easily give you first development builds of new versions of MC which are very unstable. Just a suggestion
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TehKiti, multicraft do not supply the jar files for bukkit, the server host or yourself have to do it manually.
Do it yourself
Ask your host to have custom jars, once done. Upload the latest bukkit jar to the JAR folder, and in multicraft, under custom jar file textbox, insert the name of file.
Normally the host would update it within a few days, unless you have a crap host which many are out there. Submit a support ticket asking for them to add it if they do not approve of custom jar selection.
If you have the standalone and want to update it do the following.
Download the jar from bukkit.
Copy the config file where the jar is located.
It will be something like craftbukkit.jar.conf or craftbukkit.conf.jar
Rename that config file to the exact same thing as the jar you downloaded and make sure that conf.jar/jar.conf (Not sure which one) extension is on there
Edit the config, and it is straightforward
Upload it to wherever multicraft is located and then refresh the page.
If your server is hosted by a company, contact them otherwise you can't do this.