Answered My Own Question
So here is the answer to my own question
To instead configure FCKeditor manually to use CKFinder, just edit the fckconfig.js file in the FCKeditor directory and modify the following settings:
FCKConfig.LinkBrowserURL = '/ckfinder/ckfinder.html' ;
FCKConfig.ImageBrowserURL = '/ckfinder/ckfinder.html?type=Images' ;
FCKConfig.FlashBrowserURL = '/ckfinder/ckfinder.html?type=Flash' ;
FCKConfig.LinkUploadURL = '/ckfinder/core/connector/php/connector.php?command=QuickUpload&type=Files' ;
FCKConfig.ImageUploadURL = '/ckfinder/core/connector/php/connector.php?command=QuickUpload&type=Images' ;
FCKConfig.FlashUploadURL = '/ckfinder/core/connector/php/connector.php?command=QuickUpload&type=Flash' ;
Just find the fckconfig.js file under the irite folder.