Hey there, AdriaanC!
The (3Gb/s) SATA ports are SATA II and respectively the 6Gb/s are SATA III.
You need to plug your SSD in the first available SATA III (6 Gb/s) port (preferably one of the grey ports, you wouldn't need the dark blue for now).
If the HDD is SATA III (6 Gb/s) as well, then you can plug it next to the SSD (after you've installed the OS on the SSD). Don't have both storage devices plugged to the motherboard until you've finished the installation of Windows on the primary drive (otherwise you'd encounter an OS confusion).
Either way, for the mechanical HDDs it doesn't make much of a difference whether it's SATA II or SATA III, because they are limited in their throughput by platter density and RPMs which prevent them...