A 360mm radiator would be plenty for a CPU and motherboard, thickness wouldnt matter too much I think.
I advise against using the stock water-cooling options on the mobo (the Crosschill or Hybrid Water solution or whatever they call it) as its made of Aluminium, a metal that you don't want anywhere near your water-loop due to its high potential for corrosion in the presence of typical water-cooling metals like Copper and Nickel.
Routing the tubing. I would go...
Loop -> South bridge -> CPU -> VRM -> GPU -> Loop
Thats what would be the most pleasing aesthetically I think, as tubing isnt crossing anywhere. Only potential problem is how long your graphics card and how high your RAM is for the tubing run between Southbridge and CPU.