I do not believe there is an Upgrade Path from Win 8 CP to Win 8 RP. If you install Win 8 RP into the same partition as Win 8 CP it should create a folder called windows.old which contains the whole Win 8 CP OS so you can open the folder and drag you files into the new OS. If you attempt to Upgrade Win 8 CP to Win 8 RP this is what will happen. I would suggest backing up your files to a flash then installing Win 8 RP over Win 8 CP.
The cleanest installation is a Custom Install. This will format the HD. After installing your apps you can take your backup files and put them into the new OS.
In either case all your apps will have to be re-installed.