it really does not matter where items are located heat wise as you will gain/lose maybe 1 degree once everythings up to temp, watercooling hits a happy medium after about 10 minutes where its all the same temp so stick the pump where you want to.
as for initial fill priming 2 things to consider are drain and fill ports, i have drain pipes in the form of a t-piece with enough pipe coiled to allow it drain into a tub. a fill port can be lower than the highest item (your rad the same as me) but consider connectiong a spare fitting to the fill port with some extra pipe and a funnel on the top so you can have some fluid ready to draw into the pump. (from experience when it starts to draw you may get a huge air bubble head back up the pipe and splash you and everything around you so make sure you have a rag over it!!)
when i do the initial fill i use the mains switch to pulse the power until there is enough water in to prevent a dry pump.
designing a system with a pump including res top also helps with initial fill problems