It is suggesting that using ports 0-5 will result in better performance with SATA III drives. It doesn't matter, you can stick the cable in any of the ports. For your primary hard drive, I'd use 0 since that is where the BIOS will look for the primary (boot) HD.
Did you notice that all six of those SATA ports are connected to the Intel SATA controller on the Intel P67 Express chipset?
That looks like a picture of the Z68 Extreme7 Gen3 to me not a P67 Extreme4 Gen3.
The four SATA connectors to the right of the sticker are connected to the ASMedia ASM1061 SATA3 controller.
If you really do have a P67 Extreme4 Gen3 then the two SATA connectors to the right of the sticker are connected to the Marvell SE9120 SATA3 controller.
The non-Intel SATA controllers are known to be slower than Intel's SATA controller. The scan for attached SATA devices on the non-Intel SATA controller(s) happens after the scan on the Intel SATA controller hence the reason for the longer boot time.