The OP was asking specifically about a PC video card. If he/she wants to run it off the card that came with the Mac Pro, all he/she needs is Apple's TB3-TB2 adapter and then plug it in to any TB port he/she chooses.
The OP stated he/she specifically wants to run an Apple Thunderbolt Display, which only accepts a Thunderbolt input, off a PC card (installed in his Mac Pro; see the screenshot posted above). The output of a generic PC graphics card cannot be fed back to the Mac Pro's TB ports (generic cards are missing Apple's proprietary connectors). Any standard DP/HDMI monitor would run off the PC card, but not Apple's Thunderbolt Display.
I have one of these displays in my basement... it will not work off a simple displayport signal.