There are two "types" of embedded RAID on your Z9PE-D16. Either LSI MegaRAID or Intel Rapid Storage Technology enterprise. Obviously there are different drivers for each of these.
I believe you should be able to designate one or the other of these two technologies within the Z9PE-D16 BIOS. Make sure you are using the correct driver for LSI MegaRAID or RSTe.
Chapter 5 of the Z9PE-D16 Series motherboard manual has pretty good configuration instructions.