I tend to add the lit coals to the end away from the stoker (toward the cooker).
I don't think it matters much, if at all.
Consider that the whole Stoker idea is to provide much more fuel than you want to use, but to limit combustion by limiting the available air.
On a good day, you are going to get about the same amount of burning from the same amount of air without much dependency on where the fire is located in the box.
It is also worth noting that, at least in my case with a Char-Griller, the fire burns almost entirely off of the leaked air, not the Stoker running. I.e., the Stoker only runs for a few seconds out of every few tens of minutes.
In a cooker that seals better, it might run more often as the only supply of air. In an unmodified CG, it might also run more because of the heat loss that I avoid with gaskets and insulation.
In any case, the available air must limit combustion or the Stoker cannot regulate temperatures. Therefore, it probably does not matter much where the combustion is happening.