Go ahead and plug it into the RAID controller. I have
the 45 Gig IBM ATA/100 HD (and it's the only HD I have
in there) and it's plugged into that port. Works great.
I also put my DVD-ROM on the primary port of the regular
IDE controller and I put my CDRW on the primary port of the
secondary IDE controller. This way, those devices aren't
interfering with each other or the HD.
I'm going to add a second HD and I'm going to make it the
master on the primary IDE controller (it's only ATA/66) and
that's where a lot of my data will go.