That board is a little wierd because the dark blue ports are shared with the external ports. So if external sata is on (default is on) those dark blue ports wont work. If external sata is off then they will work.
For best performance plug your ssd into the 6gb white ports, Plug your DVDs and older Hard drives into the 3gb light blue ports.
As you listed it is the order, Marvell on the top closet to the CPU. Use the Intel SATA ports, if both the SSD and HDD are SATA3 then use the 2nd row or Intel SATA3 port. Marvell ports don't show-up in the BIOS.
Next, I assume in the BIOS that the ports are not Disabled and SATA is set to AHCI; note page 3-18 of the manual.
The (no hard drive found!) can refer to the other empty SATA ports, but without seeing what you see it's tough to assume.
Dont use the dark blue. Set them to External in the bios then you can use the sata ports on the back of the board if you like.
I have the same board an on mine the grey are white. Use the grey for the SSD because it is 6gb transfer speed. You can use the other grey for the HD if you like but the HD cant transfer at 6gb so it wont help.
Light blue can be used for anything but because they are only 3gb they are best suited for old HDs and CD-DVD.
CPU ; top
Marvell ; Dark Blue ; don't use and if not used Disable
Intel ; Lighter Blue ; SATA3 use those for SSD + HDD
Intel ; Gray ; use for DVD
Intel ; Gray ; blank
Just signed up so not sure if this is where I put my thanks in but needed to say that I had my ssd plugged into the Marvell ports and it's what must have been causing me to randomly BSOD because now BSOD is no more, so far thanks heaps!!!