Check the length of your CD audio cable. The CD-ROM drive cannot be further away from the sound card than the length of this cable. Watch out for intereference between drives and the motherboard. In particular, the voltage regulator on modern motherboards can get very hot in operation, and you want to keep it away from hard disk drives. In general, I try to keep drives of all sorts away from the motherboard.
Some cases have a spot for mounting a hard disk at the very top of the case.
Second, this part of the case is usually farthest from the motherboard, making it a stretch to get the cable to reach. If you have a lot of bays, you may want to decide on where to put the drives based more on cooling considerations. If the system is in a tower case that is going to be placed on the floor, it's easier for the user to reach the drive doors to change media in floppy or CD-ROM drives when they are towards the top of the case. Count the number of drives that are going into the system. Then count the number of power plugs that come from the power supply.