I'm sure that you remember these details:
An IDE or EIDE or PATA controller supports two drives -- master and slave.
Older systems typically have a primary and secondary EIDE controller.
With both PATA and SATA controllers in the same system, PATA usually gets considered first.
Linux sees PATA devices as /dev/hd[a-z] and SATA devices as /dev/sd[a-z].
WinXX boots from "the first drive on the first controller".
In my own practice, I put my best CD/DVD drive on a different controller from my most important HDD. This way read media uses one controller channel and the corresponding write disk uses another controller channel. Likewise read disk and write media also use distinct controller channels. With two PATA controllers I do this:
- PATA-1, primary drive = boot or system HDD
- PATA-1, secondary drive = alternate CD/DVD
- PATA-2, primary drive = best CD/DVD
- PATA-2, secondary drive = alternate HDD
The above is pretty olde school. Adding SATA to the mix changes things because it must allow for how the BIOS recognizes the mix of controllers and drives.
On win-doze your mileage will vary.