1. For the GMm/r^2, with or without negative sign doesn't matter. This formula tells you about the magnitude of the force that exist between 2 point masses only. To account for the direction of the force, sign convention is employed such as force to the right is postive"+". But in your examination, GMm/r^2 without negative sign is preferred because usually the question requires only the magnitude of the force between them.

2. Gravitational potential ALWAYS has a negative "-" sign in the formula. The negative sign is from the derivation.

3. Gravitational potential ENERGY is a scalar quantity. Thus the sign doesn't really matter as said by @maru&box.