Was hopping to find an answer here to your question, because I have a similar problem. I am currently running with an ASUS A8V Deluxe mobo that has 4 SATA ports but 2 are controlled by the VIA chip and the other 2 use Promise chip. In this configuration I have 2 older but quite serviceable WD 80G drives configured as Raid 0 and they have worked well for over 2 years. However 2 weeks ago I ordered a new SATA CD/DVD R+W to replace a dead IDE R+W drive. When I tried to connect the new SATA to the Promise Port the BIOS couldn't find it. After reading the User Guide very carefully I discovered the Promise controller (though it says it will accept other device types) will not recognise a CD/DVD.
So I decided it was time to do a major upgrade. I have ordered a new mobo (M3A amd770 sock AM2+/AM2) a new cpu (AMD 64 X2 6000+ Windsor) a new graphics card (ASUS en8600gt) and 4G of memory (currently only have 1G).
However I'm now having second thoughts the once again I have lept before I looked (not enough research). In reading the User Guide for the M3A I can't find any where it specifically says I can use 2 SATA ports for my Raid 0 HDD drives and the other 2 for SATA CD/DVD drives. I'm hopping that since I last upgrade, the manufactures have started to assume the there SATA ports could be used for HDD, Raid HDD, or any other SATA device you may connect. BTW the 2 SATA CD/DVD R+W devices are liteon 20X DVD Writer. Is there someone out there that has a combination of Raid and CD/DVD drives on there 4 SATA ports that can calm my fears of having waisted more money through ignorance?