Step 1: Check to see if the version in brackets beside your jar selection name on a Multicraft is a higher version than your server is currently. You can check your current Bukkit version for example by typing /version in game. If so, go on to step 2.
Step 2: Look at the jar name below the jar dropdown menu on Multicraft. After doing so, go to Files -> FTP File Access -> Login -> Look for the jar name you saw earlier, tick the box beside it and hit 'delete' at the top. Confirm, once finished go back to your server page and start/restart your server.
Step 3: That's it! Your server should now be updated to the Minecraft version shown in the brackets beside the selected jar.