The way I have it is
rad>cpu>pump>res>rad
It really doesn't make much difference which way you have it, but the way I see it is, if you start at the rad next is your CPU, so strait away heat from that is then carried into the pump (or GPU if you have one WC'd) then that is all the hot parts of the loop.
So by passing through all the hot parts, all the heat from the loop is then passed through the res and then into the rad where all the heat is dissipated.
So, when the water comes back out the rad all the heat from the all the parts has passed through the res and into the rad.
If you have the pump after the res then it has to pass through another hot part, the pump, after passing through a cool part, the res. It just makes more sense to me to have the coolant pass through all the hot parts and then out through all the cool parts.
When filling the loop the pump won't run dry if you keep the coolant topped up enough and you can turn the pump off before all the fluid is passed through. Then you just top it up again and turn it back on. Soon enough there will be enough coolant in the loop that you can leave it running. If you are using a drivebay res you can just add all the fluid till the res is full, as you fill the res it fills the tubes before filling the res so by the time the res is full there is enough coolant in the loop so that there is no chance of the pump running dry.
For draining you don't need to run the pump so there is no need to worry about the pump run dry. You can run a pump dry for over 30secs with no problems, thats more than enough time to turn it off it it does run dry.
Just my twenty pence.