Mike,
Suppose a body moves with uniform acceleration. Its position in terms of time is y(t)=y(init) + v(init) t+a/2 t2.
In case gravity is the only force acting on the body, you know that it accelerates downward, and the magnitude of the acceleration is g=9.8 m/s2. The value of g can be given with more or less accuracy, and it is different at different places of Earth, but it is always a positive number.
Before you start to solve a problem you draw a figure and show what direction you mean positive. You should choose the sign of both the acceleration and initial velocity with respect to this direction.
In the problem, y(init) is positive, and the position of the stone is always positive till it reaches the ground, where y is defined zero.
The initial velocity is downward, so it is negative, -5 m/s. Have been the stone thrown upward, the initial velocity would be positive.
The acceleration is downward, and its magnitude is equal to g, so a=-g =-9.8 m/s2. So your equation is
y(t)=y(init)-5t-9.8/2 t2.
ehild