All of these programs are through College Board. Have you called to speak with a representative to see if they have some information to share? These programs may very well cover the same material, but they are tested in completely different ways. I am familiar with the AP and CLEP test structure, but not the SAT II. I do know that if you have taken either of these subjects as AP courses and received passing scores, universities generally do not offer additional credit if you take and pass the CLEP exams. Basically they will not double up on the credit!
The nice option with the CLEP exams is they are offered throughout the year (not only in May like the AP exams). You will also know your score immediately upon completion of the computerized exam (again, not like the AP exams where you have to wait at least 2 months for your results). The CLEP exams are all multiple-choice whereas I believe the AP exams have both multiple-choice and free response sections.
Biology and Chemistry are known as more difficult CLEP exams, but if you have a good background with these subjects you will probably do just fine. What score does your university require for passing? ACE recommends a "50" but your university can set their own passing score (the scaled score ranges from 20 at the lowest end to 80 at the highest end).