You have two separate IDE channels in the MDD, one is ATA100 and one is ATA66, both are going to be fairly slow by current standards, but you should already have all the cables in there you need to put the second drive on the either channel. If you put the drive on it's own cable, this will help speed things up if you are doing copying from one drive to the other. If you are dual booting from one or the other drive and don't really plan on copying data from one to the other much, then a Master/Slave on the same cable might be just fine. The point I am trying to make, is that both drives on the faster bus may actually yield slower performance than one drive on the faster bus and one drive on the slower bus.
You might want to put one drive in the front bay and one in the rear bay on the separate cables to help keep the airflow path open around the CPU heatsink. Both hot hard drives in the rear bay may make the CPU overheat. I don't remember which bay has the cables that run to the faster ATA100 bus, I think it is the rear bay.
Also, after you move around and open up one of these older machines things tend to settle a little and the thermal contact between the CPU and heatsink might get disrupted. Might be a good time to clean and replace the thermal paste at the CPU-heatsink contact point. You may notice a difference in lower fan speeds and less noise when the heatsink is doing the job properly.
