I'm sure the manual would told you how to connect your HDD to it, but in case you don't have the manual:
I don't have a VP6, but I can answer your question(s).  Yes, the VP6 does have an ATA100 controller.  The only thing you would need to achieve that speed is the correct IDE cable (ATA100 spec.).  You need to purchase one if it doesn't come with the HDD or motherboard.  You can purchase  it @ 
www.pccables.com or a local computer stores.
From the look of the mobo at 
Abit's site, connect your IBM drive to the regular (non-raid) primary slot (white slot next to the edge of the mobo.
The HDD should have been set as a master by default.  You need to set the CDROM drive as a slave drive if you're going to hook them up to the same cable.
I would prefer having the HDD set as primary master and CDROM as secondary (the other white slot) master.  You would need two cables for this.
HTH,
-khanh