the question will tell you or imply the direction of travel, so you'll know when its negative. often you have to apply conservation of momentum so direction matters. e is just a ratio but cannot be negative.
so if e=1/2 against a wall, and its approaching at 5ms/1, the rebound speed will be 2.5m/s. depending on your sign convention, its velocity is now negative velocity.
but sometimes objects may collide but continue to move in the same direction so you cant assume its negative.