ATA33 controllers onwards generally can handle a mixture of speeds so I assume you have an ATA-100 controller so it should be able to handle both of them at their own speeds.
Of course it is gonna be slower than having them on totally seperate channels but it's a much better idea that mixing hard drives and cd-roms. Cluck it in and check that just after boot they are coming up as ata-66 and ata-100 to make doubly sure.
Corm