the SATA drive will be controlled by the card while the IDE drive will be controlled by the onboard IDE controller.
That machine will take two IDE drives, one on top of the other and there should be power connectors for a further two drives of whatever flavor you like.
P
My PowerMac Yosemite tower is getting old, but not slow enough to replace. Put in an upgrade card from OWC to jump from 400MGhz to 1.4 GHz. Now I want to put in a larger hard drive as the 20 Gb ATA drive that came with it just isn't working out so well now.At this moment I am using 10.2.3, but for Christmas will be upgrading to Tiger, 10.4.6.
I know about the gigabyte limit on the hard drive and plan to buy a PCI card to plug the new drive into. Will the 20 Gb drive still work off of the original wiring, along with the larger SATA drive? I want to hand over the 20 to my daughter while I put my stuff on the larger drive, so I want the two to play nice together.

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic