Download the server file, then just upload. I don't use MossyCobble, but it claims to have nice GUI.
[Edit]
Checked it out, you can only have a Bukkit if you are a Power Customer. ($35.00+)
[Edit2]
Found this. Again, only Power Customers.
http://mossycobble.com/clients/knowledgebase/10/How-to-install-custom-Mods-and-none-recommended-Bukkit-versionsPower-Only.html