Boot Disk problems using AIC-7899 Controller

I have a spare PowerEdge 1400SC that I want to use as a new file server running Windows server 2003.  I'm trying to build it using a Quantum Atlas V 18.3 SCSI hard drive as the boot drive running on the embedded Adaptec SCSI controller (AIC-7899).  I also have 4 Fujitsu drives configured as RAID 5 on the PERC controller.  I'm struggling with having the OS installation or the DELL Open Mange Server Assistant installation recognize the Quantum drive as a bootable device.  Here's what steps I have taken thus far:

1.  I used the respective SCSI utilities (Adaptec CNTRL-A and PERC CNTRL-M) to prepare, format and initialize the drives.  This process completed with no error. 

2.  Using the Adaptec utility, I specified that the Quatum drive should serve as the boot device by specifying the appropriate SCSI channel and SCSI ID for the drive.  On boot up the SCSI BIOS for both sets of drives properly identify the physical and logical configuration and do not report any errors. 

3.  I then ran the DELL Open Manage Server Assistant program - primarily so I could re-instate the Dell Utility partition on the boot drive.  The first time I ran this, the Quantum drive was properly identified as a suitable boot device.  I completed all the survey information regarding OS and etc. and as instructed in the utility I rebooted to begin the OS load.

At this point the server hung showing the message - "Setup inspecting your computer's hardware configuration... "

I then attempted to start the Server Assistant process again - but now no boot device was found.  I also tried loading the OS from media, booting to DOS and etc. but in every case no boot device is found.  However, the Adaptec and PERC SCSI BIOS are still properly identifying all drives and reporting no errors.

Any ideas as to what I can do in order to have the Quantum drive be recognized as a boot device once again?   Also, my desire to use the Adaptec controller for the boot/OS drive and the PERC controller to manage the file storage is to maximize server performance.  Does this approach make sense?

Thanks for any suggestions or advice,

Dave