Doesn't really matter, its just that if you put the system disk which will contain Windows (in your case the SSD) in port 2 and another HDD in port 1, your windows system drive could be called D: instead of C:, which is kind of annoying.
Putting the system disk first should resolve this, and any 'secondary' HDD you connect doesn't matter if its port 2 or port 6. Only some motherboard have 'extra' ports that can be slower than the regular chipset-powered SATA ports, but in your case you only have 6 chipset-powered ports which all have equal speed.