The settings for which editor to use are stored in the web.config file.
When you upgrade to DNN 5 you will need to compare the contents in the web.config file and make sure you use the settings for the FCKEditor which will be in the DNN5 web.config upgrade files and remove the settings for the RAD editor.
CREATE A BACKUP of your web.config file before doing this
CREATE A BACKUP of your entire installation files + database before attempting an upgrade as well
I would suggest for your needs, use the manual upgrade method. In the future for further upgrades once you have configured the web.config file for FCKEditor you will be able to upgrade using the auto method.