During the installation process CKEditor will check for the existence of the FCKeditor module and copy all FCKeditor settings, profiles etc. (to save your time, just disable the FCKeditor module during the CKEditor installation. If you uninstall the FCKeditor module before installing CKEditor, all FCKeditor settings will be deleted from the database and CKEditor will not copy them).
After installing CKEditor you may uninstall the FCKeditor module.
If both modules are enabled (CKEditor and FCKeditor), you may get JavaScript errors when both editors will try to attach to the same textarea. If you are having problems after upgrading, make sure that this situation did not occur.
Apart from the information above, installing CKEditor is just like installing a new module, so be sure to follow the installation instructions listed above.