I had a similar setup on a A8N-E. I disconnected all the HDDs, except for
the SATA drive I wanted to boot from, then installed the OS, drivers,
etc..., then reconnected the other drives and no problem.

Have a large experience on reinstalling Windows on multi-physical-disk machines
(SCSI included).

All is fine in these cases. The existing volumes are alive and visible in the
new reinstalled Windows automatically - with random drive letters though (can
be changed).

Be sure you understand well the SATA mappings on your mobo. On Asus mobos like
P5P800 (i865PE chipset, P4-Prescott CPU and AGP) the 2 SATA outlets are either
mapped to the 3rd host controller Primary Master and Secondary Master, or as
Secondary Master and Secondary Slave to the second PATA controller (secondary
PATA itself is disabled).

The latter mode is slow (disks are inter-dependent on each other on ATA
register pool and cannot run IO in parallel) but requires no drivers and runs
on MS-DOS+BIOS.

The former mode is better, but require the drivers, which are automatically
provided by XP and later, but not by w2k.

I would not install any vendor's drivers for ATA controller anyway, provided
the MS's out-of-the-box drivers are running OK in terms of performance and CPU
load. MS has (with XP SP2 at least) the out-of-the-box drivers for the majority
of modern hardware (at least for SATA facilities in Intel chipsets).

As about UNIXen - their installation only touch the disk you have selected
(must be a primary boot disk in BIOS I think) and does not touches any other
disks at all. You will need to add /etc/fstab entries manually letter to see
their filesystems in UNIX.

--
Maxim Shatskih, Windows DDK MVP
StorageCraft Corporation

http://www.storagecraft.com