Hi Jennifer!
You can make notes in the CPT book for the CPC exam. They must be handwritten though, no sticky notes or homemade tabs or anything like that. I had actually written a lot of notes throughout the sections of my CPT book and I had no problem when the proctor checked my book. While I haven't taken the CCS yet, I do believe you can not have anything written in the PCS book. They are more strict on that then for the CPC exam. Hope that helps!