I currently have a type C visa (mult-entry for 90 days) issued from 30-07-2016 until 12-11-2016 by the Netherlands embassy. I want to travel on the 07-11-2016, my first entry port will be France, does this mean the duration of my stay will only be 6 days?
Yes. If you want to stay after your visa expires, you should apply for another visa before your trip (it is not possible to apply for a visa once you're in the Schengen area). If they grant it, it will be valid from 13-11-2016. You will still need to comply with the 90/180 rule, independent of the fact that you have two visas.
The country to which you apply should be the main destination of your trip. The port of entry is not relevant unless your trip doesn't have a single main destination.