When a ball is thrown upwards, the height at its peak is defined as y, while the initial height from which it is thrown is y-initial. The coordinate system can be set with the origin at ground level, making y=0 at that point. The maximum height reached depends on the initial velocity and the time taken to stop ascending, calculated using the equation y(t) = y(0) + Vy(0)*t + 1/2*ay*t^2, where ay is the acceleration due to gravity. The time taken for the ball to descend is not equal to the time taken to reach its maximum height if released from a height above ground level.