Screw it with the heatpipes facing away from the PCIE slot and you should be fine. The Intel heatsync mount is relatively square-shaped, you should be able to get away with it just fine. http://elchapuzasinformatico.com/wp-content/uploads/2014/02/Raijintek-Zelos-15.jpg
There's an image of it post-install. Those heat pipes don't stick out as much as you'd think they would. You probably have more than enough clearance for the GPU if you faced them that way, but since there are no heat spreaders behind your CPU, i'd say point them towards the top of the board and give yourself the extra room if you can.