Do both. Spend most of the time working on flat ground, but incorporate the inclined treadmill in 1-2 times a week.
Also, do 1-2 sets of squats a week, and do farklek runs to build endurance.
But rememeber, your son is still too young to be over doing it. Just make it fun for him now, and encourage him to start working extremely hard once he is ~16 years old.
The best thing he can do at his age is just go outside and play. ;)
Flying Australians or Box Jumps are awesome for toning the legs.