There is no such option in BIOS to change the boot order of SATA controller.
However you have an option to change the boot order of HDD, or RAID array.
Go to Boot Device Priority Menu.
You will find hard drive model or the RAID volume listed in the "hard drive order ".
Set the HDD/ RAID volume which contain OS as the first one.
You have to press '+' and '-' key to change the hard drive order.
To add in, if you would want to disable E-SATA controller you can disable E-SATA ports.
The machine will not boot up at all if any drives are plugged into the sata card. I cannot even access the boot menu. If I unplug all four drives connected to the card, the machine will boot up and I can access the bios and boot menu. After the machine starts, I can plug in the drives and they are immediately recognized. How can I make the machine boot past this card (with drives connected to it) to the main drive withe operating system installed on it?
And by the way, the configuration I have set in bios is ACHI, with blue sata ports enabled as ACHI and eSATA enabled as RAID.