Yes they can be used as regular IDE connectors. But usually only with HDD's. CD drives tend to have problems when connected the IDE3 and IDE4 connectors.
Edit: Here's a little more info on using the IDE3 and 4 connectors. This comes from the KT7A-RAID Faq.
Make sure that the Highpoint controller is enabled in the Integrated Peripherals screen of the BIOS. In order to boot off a disk connected to the Highpoint controller, use the RAID option as the boot device in the Advanced BIOS Features Setup menu of the BIOS. Don't worry about the word RAID - selecting this does not enable RAID