That would be 8 , USB 3.0 (Also compatible with USB 2.0) & 12 USB 2.0 ports
so yes the two USB 3.0 ports on the front of the HALF X case will be connected to the midboard ( same with the two USB 2.0 on the front)
& the rest will be at the back ( at leased its this way on mine ) - doesnt look like you need that PCI card to me - good thing , more spacing between the top & bottom cards for SLI , sure you will see setups where they have 2 or 4 of them litteraly on top of eachother & say "of coarse it wont overheat" - yes maybe for half an hour or so - keep at leased half an inch between cards is my way of looking at it & anything more is a bonus.