Thanks for all the helpful replies 
I attached my electrical circuit for dividing the two voltages.
I thought about using a Diode. Where would I put it in the circuit?
About the electrical circuit in the charge controller I will have to look in the documentation but I assume that it is not totally trivial 
Yes I assume they do not have a common earth, I measured before with a multimeter as well and I have different Voltages, depending on the charge state on the battery.
Thanks again!