Though we have a new equation to use to calculate the gravitational potential energy between point masses, whether the potential energy is increasing or decreasing is still built on the same concept we used when the gravitational force acting on an object was constant.  The gravitational potential energy increases when you move against the gravitational force.  Though the gravitational force between point particles isn’t constant, it is still always trying to pull particles towards one another.  Therefore, the gravitational potential energy increases when you pull the particles apart.  You have done positive work to move them apart, which has been stored in an increase in the potential energy available to the system.  If you move the particles towards one another, the gravitational potential energy will decrease as the particles have moved with the gravitational force pulling them together.  If you let the particles go, the energy stored in gravitational potential energy will be converted to potential energy as the particles moved towards each other.  Conservation of energy will let you determine the speed each particle is traveling with after they have moved through a given distance.