A lot of controversy so here's an example...
Say you have charges Q and q that are attracted to each other.
What is the force you'll have to apply to maintain the system's potential energy?
Say at distance r they apply force F on each other.
You apply force F on q to hold it in place. But Q is still moving towards q. So you have to apply another force F on Q to keep it in place too. Thus at each point, you have to apply 2F force on the system. This is what the confusion was about.
The change in potential energy would be the work done from there on. So say on a particle with charge q you apply a force F + dF, just above F so that you move it further apart.
To change a particular configuration... the net force you apply is the force to maintain the configuration in the first place + the extra dF force you apply (which is almost 0).
That brings us to 2F + dF which is just 2F for all theoretical purposes.
There you go, the work to be done is thus 2F*dx for distance dx.
So the work done to change the configuration must be 2kQq/x. Bringing charges from infinity, the work IS the potential energy of the system.
Now I myself don't know if that is right, which is why I put it up as a question. WHAT AM I MISSING?
Conclusion (EDIT):
Say we apply force F on both particles (total force being 2F) which is just enough to move them apart. They both move distance dx so the total work done is 2(Fdx) and the total distance they moved apart is 2*dx (they both move dx dist. in opposite directions). That would mean moving them dx distance apart, work done is Fdx, integrating it would imply that change in Potential energy to bring them distance r apart would be kQq/r...
So to bring them at distance x from infinity, we have to move them half the distance each while applying equal force on both Q and q. Which just mathematically happens to be the same as applying force F on q and moving it all the way to x distance from Q.
Thus, U = kQq/r is correct. But we do have to apply force on both particles if we practically have to get them into a configuration. Just that we have to only make them move half the distance each.
I hope it makes sense for everyone now.