Just don't use the 2 white SATA II ports. The 5 orange SATA ports are via the intel ICH10R chipset/controller.
Don't install the specfic drivers for the JMicron controller, either. Let the OS install the "generic" driver. I believe it called "JMicron JMB36X" via either the mobo chipset CD/DVD, or the Asus website, still don't use it.
Set the SATA ports in the BIOS to ACHI to get the best performance for both drives.
You didn't mention what kind of Optical drive you have: IDE or SATA. Some optical drives won't work via SATA in ACHI mode.
If this is so, then use the JMicron ports, and set them to IDE in the BIOS. Still no specific driver install. If you have an IDE optical drive, same way. I have no problems set this way.