[Martoch]

It doesn't matter where they are physically located inside the computer...the IDE cable attachment and jumper settings are what matter.
Look at this picture...it shows the various jumper settings for your drives. You will want to put your DVD drive on the end of the IDE cable, which has the oval around it in this picture. Your CD drive will be attached by the connector with the rectangle around it in that same picture. Make sure your DVD drive jumper is on the MA (Master) pins, while your CD drive is on the SL (Slave) pins. If that doesn't work, move them both to the CS (Cable Select) pins. Of course, you will want to make sure you power off while making any of these changes.