The two pcie3x16 slots get their pcie3 lanes from the cpu which only has 16 to give. So if you populate both of those slots you will drop down to x8/x8 mode.
The x4 slot gets its lanes from the 'Northbridge' and is pcie2 so no problems there
Will it fit under ? Cant say, dont know what cable or GPU you have but i doubt it from looking at the pic of the motherbd.