So what I did on my 3.5" nodes was:
SATA III 1 - SSD1
SATA III 2 - SSD2
SATA II 1 - HDD1
The Intel 602 PCH if you are using SATA SSDs works well. You just do not have enough 6gbps ports because that was the generation where Intel added a 3gbps SAS controller on the PCH.
Which cables did you use? I am also using a HBA and see that this is the cable that is referred to 85C6Y