Perhaps a silly question, but a question.

I have seen many posts about setting up servers using craftbukkit, but almost nothing about implementing the bukkit API.
The whole server does not need bukkit to run at all.
Am I missing something?
On another note, I have also been attempting to setup server commands, as well as other plugins and the commands that are associated with them. Currently, I am trying to get "WorldEdit" and the guard version as well. BUT...
Editing the group.txt allowing myself to use every single command, does nothing.
Apparently kits is also supposed to work, but it only seems to with other plugins.

How does one go about doing this, or at least using bukkit as the API...