For a system like that, I would do mostly what you've already figured. Boot from the onboard IDE with a dedicated drive (or compactflash card or DiskOnChip module etc..), and then use the PCI SATA controller to implement a RAID array in software.

The choice would likely fall down to RAID1 (best redundancy, simplest recovery, lowest capacity) and RAID5 (much faster reads, higher capacity, most complex recovery [but not *that* complex!]).

If the onboard IDE is a real drive, then I'd install the O/S there. If the onboard IDE device is a flash thingie, then I'd likely just put the /boot partition there, and everything else onto the RAID array. In fact, the latter is what I often recommend.

Cheers