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i think that if you put it on the bottom,you can controll the balance better.
I know nothing about balancing robots, but I would tend to think having the mass at the top would be easier to balance. Try to balance a pencil on your hand, then try it with a weight on top (blob of clay), then a weight near the hand - you'll find its easier with the weight at the top. I imagine the same would be true for a robot (ie, inverted pendulum)...
Your are right cr0sh
the robot acts as an inverted pendulum and works better when the weight is high (it increases intertia and allows more reaction time).
Try to balance a broom in the palm of your hand and see which side is easier to balance.
However, PID parameters need different tuning