I would leave it closed. My thinking is to allow any extra air pressure generated by the two front fans to force the air across the GPU towards the rear, rather than allow it to flow up.
I know on my R4, there wasn't much room above my heatsink. I was able to fit a fan on the floor in front of the PSU (but it was only an old 80mm that I had laying around doing nothing).
Thanks for your help. I will close them up.
With the remaining fan, I will try to put it on the side and see how it behaves. As for a bottom fan, I will look for something smaller, maybe a 120mm will fit.
As of now the system is booting and all looks ok.
Word of WARNING: The end sliders on the PCIe slots slide. I broke one thinking it would move sideways like on my old setup.
NOTE: The PCIe 1 slot is blocked by the Cooler fan snapping metals. Either bend those or use the other slots.