You would need to manually set up RAID so the two drives will remain separate by default. It also may not even be possible to RAID the two drives if the SATA and IDE are on different chipsets, I don't quite know how the P5Q breaks them out. I'd say you're safe in not having them RAIDed automatically.
Edit: I think software RAID like in Windows would be possible to RAID drives on different chipsets... again, this is not an automatic process and requires you to manually select the drives and configure the RAID.