Grab a USB stick and start plugging it into ALL of the ports with IORegistryExplorer open and you will see which port is which and create a list. Here is what mine ended up looking like when I was getting USB3.0 to work with El Capitan, the unused ones are all internal headers that I am not using:
USB2 Mapping
- HS01 - unused
- HS02 - unused
- HS03 - ASM107x 4 below WIFI
- HS04 - ASM107x 2 beside RJ45
- HS05 - Top Left - Keyboard
- HS06 - Top Right - Mouse
- HS07 - unused
- HS08 - Front Audio
- HS09 - Front Left
- HS10 - Front Right
- HS11 - unused
- HS12 - unused
- HS13 - unused
- HS14 - unused
USB3 Mapping
- SSP1 - unused
- SSP2 - unused
- SSP3 - ASM107x 4 below WIFI
- SSP4 - ASM107x 2 beside RJ45
- SSP5 - Front Left
- SSP6 - Front Right