The difference between the two exams is length and content. I also have taken both tests, and I can give good advice since I did pretty well on both of them (5 on AP Test and 720 on SAT II). The AP Bio test is 3 hours long and includes a free-response section with 4 questions as well as 80 multiple choice questions. The SAT II as I recall has actually 100 questions. The first 80 are universal for Biology, but the final 20 depend on your choice of Bio E or M. For myself, I took Bio E, because I felt it was easier. To prepare for the AP Test, use the CliffsNotes AP prep book. I also used the same prep book for preparing for the SAT II, because I knew the AP test was more comprehensive and more difficult than the SAT II, so it is better to have the most knowledge possible.
So, in essence, I would suggest you use the CliffsNotes AP Biology Book to prepare for both tests, and I would take Biology E. The difference between the two tests is that the SAT II lasts 1 hour, in comparison to the 3 hour AP Bio Test, which also includes a free-response section.