Sorry, but I may be confusing both of us. Are you going to use one or two Blackmagic devices? I may have misread your intentions. See here regarding GPU requirements for the device:
UltraScope and Desktop Video Products – Windows PC Minimum Graphics Cards Requirements
UltraScope
Blackmagic UltraScope requires a graphics card that supports Open GL 2.1 or better and have a Texture Fill Rate of >22,000 MT/s (22 GT/s). The following PCI-Express graphics cards have been internally tested for use with Blackmagic UltraScope though it is expected newer cards will work without problem:
nVidia GeForce 9800 GT
nVidia GeForce GTS 250
nVidia GeForce GTX 275
nVidia GeForce GTX 285
nVidia GeForce GTX 550Ti
nVidia GeForce GTX 570
nVidia GeForce GTX 580
nVidia Quadro FX 4800
ATI Radeon HD 4650
ATI Radeon HD 4670
ATI Radeon HD 4680
Suitable graphics cards can be purchased for less than US$100. More expensive graphics cards are no guarantee of compatibility as the features may differ from those above. Other graphics adapters that have a similar specification to those above may work, but these are the ones we have tested in house. Most cards newer than this will work.
So, you could use a flexible x16 to x16 riser/extender from the x16 slot on the mobo for a GPU and the x1 riser/extender for the BM device.
You attach the GPU/BM card to the adapter cable and then mount the device into the case slots. There are retention tabs at the bottom and a screw at the top of each slot opening to hold devices in place.