Any Ewald scheme (for quantum calculation this is also known as Poisson Solver) for periodical charged systems, includes automatically the compensating background charge.
The energy of a periodical charged system, without background charge, is undefined (the series 1/r is not converging for systems with a net charge different from zero - actually, in general, this series is only conditionally convergent but not absolutely convergent).
I don't really understand your claim (and didn't check the paper you mentioned) - but there is nothing special in cp2k compared to other codes doing Ewald (cp2k, cpmd, quantum espresso, etc..).. So the answer is:
there is no section to activate to have the compensating background charge to have an overall neutral simulation box : simply run a standard setup for a 3D periodic system (without decoupling) and you will get automatically this term in the energy.