The main difference between the two types of nanoparticles you are talking about is the order of the carbon atoms. This order should be able to be distinguished in either XRD or TEM experiments. CQDs will exhibit a multilayer graphitic structure, whereas the CPDs will often resemble more of a crosslinked pattern. The CPDs may also not be fully carbonized, in which case you could exploit their hydrophilic surface properties to separate them and then perform optical analysis.