Take a look at this website:
http://en.wikipedia.org/wiki/AT_Attachment#Two_Devices_on_one_cable_-_speed_impact
In short, two hard drives on the same chain shouldn't make much
difference. Here's the configuration I'd recommend:
Primary master - fast hard drive
Primary slave - slow hard drive
Secondary single/master - CD/DVD-ROM
If you're using a Pentium-II or older, this is the configuration to use
if you want to get maximum performance out of the fast hard drive, and
don't care about the speed of the slow hard drive:
Primary master/single - fast hard drive
Secondary master - slow hard drive
Secondary slave - CD/DVD-ROM
I usually set the faster device as the master, but it's just personal
preference. I don't think it matters.
Mike