Bukkit is a server wrapper, and the 'mods' for it are called plugins. If you want to install plugins for Bukkit, create a folder where you downloaded Bukkit and name it "plugins", then just place all the plugins that you download into that folder. Keep in mind which version of Bukkit that you have and which versions of it that a plugin says it works with. I use a small text file with all the version numbers of my stuff for that reason. For more info on installing Bukkit, look at my post about getting started with a server here.