Functionalizing graphene beyond its intrinsic properties has been a key concept since the first successful realization of this archetype monolayer system. While various concepts, such as doping, co-doping, and layered device design, have been proposed, the often complex structural and electronic changes are often jeopardizing simple functionalization attempts. Here, we present a thorough analysis of the structural and electronic properties of co-doped graphene via Raman spectroscopy as well as magneto-transport and Hall measurements. The results highlight the challenges in understanding its microscopic properties beyond the simple preparation of such devices. It is discussed how co-doping with N and B dopants leads to effective charge-neutral defects acting as short-range scatterers, while charged defects introduce more long-range scattering centers. Such distinct behavior may obscure or alter the desired structural as well as electronic properties not anticipated initially. Exploring further the preparation of effective pn-junctions, we highlight step by step how the preparation process may lead to alterations in the intrinsic properties of the individual layers. Importantly, it is highlighted in all steps how the inhomogeneities across individual graphene sheets may challenge simple interpretations of individual measurements.