If I bought that sata controller card and put it into the 2.0 PCI slot and plugged in my 3.0gb 1tb Samsung HDD, and my sata DVD drive would it boot windows and work correctly? Also if it did work would the performance be just as good as the on board sata, sources online say its better others say sata controller cards aren't?
You should check on your MB, because it shows 4 SATA II ports an 2 SATA III ports coming off your Intel PCH.
Make sure the controllers for the the SATA ports are all enabled in the BIOS
I can't imagine all 6 SATA ports don't function properly. You can connect your Samsung HDD to SATA_1 and DVD to SATA_2, or Samsung to SATA_3 and DVD to SATA_4, or Samsung to SATA_5 and DVD to SATA-6. It won't make any difference in the speed because your attached drive will never saturate the SATA II ports if used.
Always place your boot drive before the DVD drive, and preferable in SATA_1 as numbered by ASUS.