Well, you shouldn't but sometimes it just makes the calculating easier. Like if you had a question that asked how long will it take for a ball to fall 5 m. You can think of it as +5 m and +10 m/s^2 or -5 m and -10 m/s^2. It all depends on your perspective.

But to make things easier, try and always use -10 m/s^2 and make sure your distances and velocities correlate with up being positive and down being negative.

Also, on the MCAT use 10 instead of 9.8. You can't have a calculator and it makes calculations a whole lot easier if you round some.