Unusually the PSU would be up top on the case, since heat rise this make much sense for the PSU fan to suck up the warm air and blow it out the other fan. I cant picture having a PSU behind or under the MB unless it was equip with an air duck on the side to suck warm air out. But I dont think itll damage the motherboard if it doesnt physically contact it.
Thanks Law for the reply. There will be a sheet of 1/8" Lexan between the mobo and PS. The mobo and PS will be mounted on 3/16" nylon spacers on either side of the Lexan. I will have a few(lol) AC fans blowing across the mobo and PS with ducting. It will be much better than stock (and a LOT quieter as well) Basically the sides of the case will be made out of the Hex Mesh I used in my Ultra Blue comp.