Where to put bukkit.jar?

I've been using Craftbukkit on a new server for a few days now with few issues. However, recent plugins haven't been working so well and I'm wondering if it's because I've only been updating craftbukkit.jar and not bukkit.jar.

When I update bukkit.jar where do I put that file? Does it go in the same folder as craftbukkit and, if so, what do I name it?

Also, I've seen several references to editing server.properties to enable and disable plugins - I don't see any reference in the file to this. How does one accomplish this?

Thanks!

 

No, you just need to update craftbukkit.

You delete/remove the .jar file from the plugins directory to disable. You put the .jar file in the plugin directory to install it. Nothing more, nothing less.