Optiplex 980 MT Windows Reinstall / SSD Upgrade / SATA 6gb

My Enterprise Grade HDD have failed  after 7 years of use.

BACKGROUND

The boot drive is connected to SATA0 and WD SATA 3 6gb drive connected using the blue cable to Sata 0 which i also believe is the only sata 6gb/s port on the mother board. (optiplex 980 mt)

The Second HDD is connected to SATA1 @ 3gb/s 

I know that HDD will never even reach 3gb/s but its nice to know that the optiplex  has 1 stata/6gb port.

I am not using RAID at all however in the bios i noticed that in SATA OPERATIONS / Raid is set to On = "sata is configured for RAID on every boot" the machine was pre configured like this for years and i never had any problems.

THE UPGRADE

 I installed a Samsung 860 EVO 250gb and connected it to SATA 0 which is the blue port on the mother board, i had disconnected the old boot hdd.

I changed the bios to RAID AUTODETECT / AHCI  , instead of the RAID ON ( i thought this made sense since i am not using RAID)

I reinstalled windows 10 on this new SSD, and all is working well.

Samsung Magician and various other software tools like HWINFO is telling me that the SSD is connected @ 3.0gb/s instead of the 6.0gb/s. I am also getting read speeds of only 250MB/s vs 400 or 500mb/s if the ssd were connected to a SATA 6gb port.

My question is if i set the RAID ON, the drive will be controlled by the RAID controller instead of the AHCI BIOS, does this effect the SATA 0 port speed?

What i did then may have been foolish which was was to change the bios to RAID ON, and i got a BSOD error "unable to boot"   After a few restarts and switching the bios back to AHCI windows 10 now loads, but the SSD speed is connected at only 3.0/gb

I am not too concered about this as the SSD is still far faster then the aging HDD, but why would the HDD connect at 6gb/s (albeit have slow transfer rates) but the SSD connect only at 3gb/s

I am not using RAID at all, but i wonder if utilizing the RAID intel software controller does that activate the 6gb port in any way?   I will have to reinstall windows to test this out as i remember when my HDD was connected according to HWINFO tool it showed it was connected at 6gb/s (even though the transfer speed was much lower due to the spinning hard drive)

P.S the bios has been updated to latest MAY 2018 A18.

Thanks for your help.

RISHI