I've had a few issues trying to get fckeditor to upload images to the folder I designate. Finally cracked it, here's an extract from a web.config file:
</system.web>
<appSettings>
<add key="FCKeditor:UserFilesPath" value="/GuitarShop/UserFiles/" />
</appSettings>
</configuration>
This sets the upload path to :
(root)\Inetpub\wwwroot\GuitarShop\UserFiles
