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The hard drive / optical drive have jumper settings, not the motherboard. PATA has jumper settings, but SATA do not require any. The diagram of the setting is drawn on the hard disk itself below the serial number etc. For SATA, look on the motherboard for the SATA ports. Each port will be named as like SATA 0, SATA 1 etc. If you want the hardd disk to boot first, plug it in SATA 0. and the next device in SATA 1. However, you can also set the first and other boot device from the BIOS itself, in case of SATA.
Server 2008 is not detecting your drives, because it does not have drives for what ever hard drive controller you are using. You will need to determine which controller your drives are attached to and load the appropriate driver during setup. I believe this system has built in SCSI and SATA controller and often shipped with add - in storage cards. Our came with a promise sata raid controller.
Dear Fried its possible.. Go the Boot Menu at your BIOS ( For go the BIOS Press DEL at startup your system) there you may se Hard Disk Priority Option. There you can change Hard disk Priority... you may need setup your sata as first one..
You must enter setup at boot and select the CD/DVD as first boot. Then ensure that the BIOS settings have SATA enabled. When CD/DVD is first boot watch the screen for 'press any key to boot from cd' message is displayed. The boot screen will say how to enter setup. Typical buttons are F2, Delete, F1, F10 -you did not say which manufacturer. OEM trumps mobo maker with BIOS setup.
Check the bios to see if it made the pata drive primary. If it did the system will try to boot off of your backup drive and you could think that it is not seeing your sata drive. If that is the problem you must go into the drive configuration and make the sata primary.