No problem, it's an important and non-trivial question.
It is actually easy to get confused about this way of introducing "doping", because in actual fact we don't dope at all! We could of course, include actual donor or acceptor atoms, like P or As in Si, to achieve a doping effect, but it becomes very difficult to control the concentration in this case, plus the position of the dopant might matter a lot. Therefore, we focus on WHY we dope, the answer being we want to shift the Fermi level closer to the valence or conduction band. But we don't have any control over the Fermi level, it's adjusted self-consistently, thus we need to control it via charge. But, if we just introduce free charge in an NEGF calculation, it will leak out of the system, since there are no net charged cores to retain the electron (as would be case with real dopant P or As atoms). So our only remaining choice is to create "fake" charged atoms, which if we localized the charge to a single atom would be exactly the same as using real dopants. But we can be smart and spread out the charge over several atoms, and thereby control the doing concentration with arbitrary precision. Now, by adding a net positive charge in a region, we actually attract electrons, which are free to float in from the infinite reservoirs (the electrodes), and in this way we achieve n-doping, and opposite for p-doping.
So all this is to say, the doping is an effect of the compensation charges, not the other way around. And therefore, you should not change these charges. Also, it is important to be aware of the amount of compensation charge added, and how this relates to the doping concentration. Since we have a well-defined volume of the electrodes (for 3D cases, at least; it's a bit trickier for 2D), the amount of charged placed on each atom is the desired doping concentration times the volume of the electrode, divided by the number of atoms. If you change this number, you change the doping concentration. This gives a number, the charge per atom, and we can use this both for the atoms in the electrode and those in the central region, for the region of space where we want to have the same doping.
It is essential for good convergence to use the same charges near the central region edges, but If you for instance want the middle of the central region undoped, it can be a good idea to taper these charges towards zero slowly, rather than have a abrupt change to zero at some point. The same technique can be used for a p-n junction, although in practice it seems to work with an abrupt change there, at least for a simple Si p-n case (see our tutorial on this, which notably uses tight-binding; it might work less well with DFT).
I hope this gives a good picture of how we actually use the compensation charges to control doping, and thus your question hopefully answers itself. If not, it is probably better you provide a concrete example and specific system.
