in a perfect world you would, mount 2 140 mm fans in top and bottom to create good chimney effect in the case.
the CPU gets a tower cooler with fan blowing upwards to support the effect.
the GPU gets a huge 3 slot DHE cooling system with another 140 mm high pressure fan and air duct from the bottom of the case.
or go with riser card, let it breath from side panel...
while SSD + HDD are placed somewhere close to ari flow...
sure there are other cooling concepts - but the apple trash can (mac pro) and one of the latest Brix (the high one) show very well how to do it with minor volume, you might want to transfer it to larger scale.
this all is assuming you prefer air and low noise cooling, like i do
p.s.: do not forget to plan dust filter for intake fans!