http://www.promise.com/techsupport/Faq/FT66.htm#q3 
Q3: How do I boot from the FastTrak66?
A: There is an option in the FastTrak66 BIOS to make an array bootable.  Make sure you set this option to whichever array you want to boot from.
There are two ways to make the FastTrak66 be the bootable device. One way is to make sure there are no HDDs on the motherboard controllers.  The motherboard will not find a bootable device, and allow the FastTrak66 to boot.
The other way is to change the Boot Sequence in your CMOS to boot from SCSI first.  Since the system will see the FastTrak66 as a SCSI controller, this will tell the motherboard to ignore it’s own controllers and allow our card to be the boot device.  Some motherboards do not allow this, so it may not be an option for you.
You MAY also be able to turn the auto-detection off on your motherboard and set all the HDDs in the CMOS to "None" or "Not Installed". This is if you have devices (other than HDDs) connected to the motherboard.
Again, this last suggestion MAY work.  Your motherboard may not allow this type of workaround.