Right now it's setup to boot int his order: 1. HD #1 2. HD #2 3. DVD Drive PS. I am using a software RAID0 setup.
its a matter of preference and practicality really I would just tell it to boot from HDD first so it will start a little faster if you set it to CD/DVD (optical drive) it hesitates for a second to recognize any bootable media in the drive only change it back if you need to re-install Windoze or need anything else that requires boot from somewhere other than c:
i always set mine to boot from cd first, f12 is my friend if'n i need to select a different boot device.