CKEditor plugin is highly configurable, see screenshots below to have an overview of all configuration settings.
Select your favourite skin or choose CKEditor as comment editor.
Configure output formatting to have a better control over generated HTML source.
Configure CKFinder or enable the old built-in file browser fom FCKeditor 2.x.
CKEditor have lots of configuration options, you can use this editor to change some files used by CKEditor instead of changing them via FTP (this feature is only available where server configuration allows it).