When we talk about potential energy of charges, the charges can never stay fixed at a place because they experience forces due to other charges. Hence we to keep the charges fixed some work has to be done. Potential energy of any two charges is the total amount of work done in the bringing the charges from infinite distance to their respective positions in the system Hence we are doing work on the charges. Potential energy is negative of work done. Whereas in kinetic energy the work is done by the system because it already possesses some energy. Hence its positive.