Consider a box placed on a smooth surface and a man is pushing it with force F. If the box moves through a distance s, work done "on the block"=F.s and is positive. If the box were moving with some velocity v and the man applied an opposing force F, the block will decelerate and stop. Here also, work is done "on the block by the man" , but F and s are in opposite direction, hence work done is negative here. Whoever applies force, does the work. If a man is moving a body up against gravity such that net force on it is 0, this means mg=Fman.
Since F(man) and s are in the same direction, work done by the man is positive and man loses muscular energy. Work done by gravity is negative since mg and s are opposite in direction. Hence, the body will gain same amount of PE. K.E. of the body will be 0 as discussed earlier( or it is unaffected, if present).