ClonyXXL is now very old and outdated as it hasnt been updated for a very long time! Today I find by far the best programs to use to detect the protection are either 'Protection ID (PID)' or 'A-Ray Scanner'. Both these programs can detect the latest protections. (Protection ID is constantly being updated but all the features are not up and running as yet but it will still detect the more popular protections)
As far as the actual backing up use either CloneCD of Alcohlol 120%. When backing up a CD using Alcohol 120 just choose the 'Datatype' (protection) that either PID or A-Ray detected. There is a little drop down arrow in Alcohol which allows you to choose the datatype.
When backing up DVD games with Alcohol there are no settings (Datatypes) to choose so its even easier.
With CloneCD (which I only use for SecuRom protected games) just choose 'Protected PC Game' as the profile.
All these programs are very easy to use just have a look at them and give them a try.
Use google to search for each program, CloneCD and Alcohol 120% have trial versions available for download, and PID and A-Ray Scanner are available from GameCopyWorld.
This is just a quick guide to using these two great programs, if I had a bit more time of would have supplied you with the links to the programs as well but i think you will find them quite easily.