Can I safely connect a USB 2.0/1.1 internal pin block to a USB3.0 motherboard header?

On page 33 of the motherboard's manual you can find the pinouts for both USB2 and USB3. They are not compatible. And even if they were compatible the physical connectors are not - the spacing between pins is different.

There are 2 "sockets" in each connector, so if you really, really want to connect USB2 cable into a USB3 socket you have to match pins manually:

• USB2 Power (5V) to USB3 VBUS
• USB2 USB DX- (or DY- for second socket) to USB3 D1- (or D2- for second socket)
• USB2 USB DX+ (or DY+ for second socket) to USB3 D1+ (or D2+ for second socket)
• USB2 GND to USB3 GND

This is a dangerous procedure so if you don't know what you're doing just buy a separate controller and use that.

You could add an internal usb hub - nzxt makes a pretty nice one called the iu01 that breaks out one into 6 headers and 2 normal usb ports and would work perfectly here.