Graphene-enhanced Raman scattering (GERS) on isotopically labelled bilayer and a single layer of pristine and partially hydrogenated graphene has been studied. The hydrogenated graphene sample showed a change in relative intensities of Raman bands of Rhodamine 6 G (R6G) with different vibrational energies deposited on a single layer and bilayer graphene. The change corresponds qualitatively to different doping of graphene in both areas. Pristine graphene sample exhibited no difference in doping nor relative intensities of R6G Raman peaks in the single layer and bilayer areas. Therefore, it was concluded that strain and strain inhomogeneities do not affect the GERS. Because of analyzing relative intensities of selected peaks of the R6G probe molecules, it is possible to obtain these results without determining the enhancement factor and without assuming homogeneous coverage of the molecules. Furthermore, we tested the approach on copper phtalocyanine molecules.