Hey Grymm428, thanks for the question (and any question is good feedback on how things could be explained better).
Only the spell effects stated in brackets of the spell description apply to the spell.
So the limitations on the Heal spell is just the range and effect die. If you cast it at a higher level then you can cast it further and it heals more. The target level doesn't apply here.
For the Missile spell (Missile (Range, Targets = Number of Missiles) then the factors that you can increase are the number of missiles you cast, each one does d6 damage. (i.e. level 1 = 1 missile at d6, level 2 = 2 missiles at d6 and level 3 = 4 missiles at d6).
Does that make it clearer?