問題
Q1
Why my TA990FXE system's HDD still run at IDE mode when I already set my SATA mode to AHCI mode and connect to SATA5 or SATA6?

The symptom is caused by BIOS option SATA/IDE combined mode set to "Enabled".
According to AMD chipset specification, when you set SATA/IDE combined mode to "Enabled", SATA5&6 will be set to IDE mode.
You can set the option "SATA/IDE combined mode" to "Disable" for all SATA port to run with AHCI mode.