I wouldn't put the CD-ROM on the same channel as the hard drive you'll be installing most of your software to, since it won't be able to read/write to the CD-ROM and hard drive at the same time.
Is either the CD-ROM or CD-RW ATA66 compatible? If they aren't, there's no way to avoid running your hard drive in ATA33 mode unless you get a PCI IDE card.
But now that I think of it, a 6.8GB hard drive isn't going to have a very high transfer rate anyway, so it probably won't hurt it to run it at ATA33.
I have a few more questions. Which hard drive is fastest (RPMs and real transfer speed)? Which hard drive do you want to install Windows on? Which hard drive will you be installing your games and such on?