this is a very interesting technical question. Unfortunately I'm absolutely no expert in this field as we work in synthetic inorganic chemistry. Thus all I can do to help you at the moment is suggest to you a few potentially useful literature references which might assist you in you analysis. For example, please have a look at the following relevanr articles:
Simultaneous extraction of nuclear and mitochondrial DNA from human blood
Article Simultaneous extraction of nuclear and mitochondrial DNA fro...
and
Simultaneous quantitative assessment of circulating cell-free mitochondrial and nuclear DNA by multiplex real-time PCR
The second article is freely avaiable on the internet (please see attached dpdf file). The first paper has not been posted as public full ext on RG. However, three of the authors have RG profiles. Thus there is a real chance that you can request the full text directly from one of the authors via RG (although the paper is a bit older).
I hope this helps. Good luck with your research work and best wishes, Frank Edelmann