3DGPU have an interesting article showing how to copy protected games and CD's. If you've ever wanted to know how to *cough* backup *cough* those types of CD's of yours lying around in case they ever self-destruct, you should take time to read this article.
The CD-MATE software is very intuitive. You start with the Recording Wizard, choose "CD-ROM to Imagefile" then on the next screen, try checking every single box in the "Advanced Options" area unless you have a specific reason not to, click the "Wizard" button and choose the "Source CD Read Type", which should list all the common protections, such as Safe Disc 1 & 2, SecurROM 1 & 2, Laser-Lock and others. Then on the Write page, select RAW+SUB Write Mode, Enable Buffer Underrun and under "Write Options" click the Write option and probably the S.A.M option.More information @ 3DGPU