Is the relation between change in potential energy and work by internal conservative force can be used even in presence of non conservative forces? We know that work done by internal conservative forces is the negative of change in potential energy of the system stored in conservative force field. But does this logic still hold when there are non-conservative forces like friction or resistance? 
Do the non-conservative forces only withdraw from the kinetic energy part and not affect the potential energy in any way? Consider for an example a system of two charges having some mass kept at a finite distance and both are free to move over a rough surface and released.
 A: Non-conservative forces change the total mechanical energy of the system, since
$$W_\text{nc}=\Delta E=\Delta K+\Delta U$$
assuming all conservative forces are internal to the system.
However, nothing from this tells us how the kinetic and potential energies change. More information is needed. For example, with a mass sliding on a horizontal surface with friction, the non-conservative work only changes the kinetic energy as the mass slows down. However, if you set up the mass to slide down an incline with friction at a constant speed then only the potential energy is changing. In each case we have the same non-conservative force, but the changes in kinetic and potential energies are different.
Of course one could argue that in the incline case that the potential energy is being converted into kinetic energy that is instantly removed from the system by friction, but at that point it's just a difference in interpretation that yields the same result.
A: The relation between potential energy and charge will remain. The total mechanical energy in a system is $E = KE + PE$. In a conservative system (a single particle orbiting a particle of opposite sign, not including EM radiation), that total energy remains constant. This is like a frictionless pendulum. If a system includes non conservative forces, that total energy declines as the system evolves. As this happens, $PE$ will be known as a function of the particle's position. $KE$ will then be the difference between (current) total $E$ and current $PE$. This is like a pendulum with friction. The gravitational $PE$ in a pendulum is always the same function of position ($PE = mgL(1 - \cos(\theta))$ or some equivalent formula). The $KE$ of the pendulum in a problem with friction is whatever the difference between the current total energy is and the potential energy of that known function of position.
Note that energy can also be added to a system. A rocket can be fired to increase a space craft's energy, thereby changing it to a new orbit. This is how orbital maneuvers are done. In between rocket usage, the total energy of the orbit is constant.
