Space concerns (needed to use as much space as possible for weight), and trying to generate more thrust in the area close to the rotational axis, where the large prop wasn't creating much. Also partially because we had the small propeller already attached from an older design.
What advantage would having more thrust closer to the rotational axis give you (as opposed to farther out)? More stability?
What hmcginny was getting at is that the front propeller produces some thrust over the 6inch propeller's diameter let's call this it's thrust density. The smaller prop produces a larger thrust density than the larger prop even though the larger prop produces more overall thrust. So with that specific combination we had, we were able to get the front's propeller's thrust for the area that is outside the smaller propeller's thrust but still maximize the overall amount of thrust for the maglev.
Common misconception is having two propellers behind each other will produce more thrust, that is not necessarily correct. Due to the fact that the air behind the front propeller is already moving at some speed relative to the maglev.
So all in all, we tried to produce the greatest thrust behind the entire maglev and since the smaller blades had a larger thrust density than that of the larger blade we put the motor behind the front motor. This also kept the aerodynamic properties of our maglev as close to intact as possible.