I've badly been looking for a way to both run an internal network server on eth0 and connecting to any kind of internet device, be it on wlan0 or a USB dongle.
That way, I can be online and browsing documentation, downloading new stuff etc. on the server but not depend on a static configuration but still use Network Manager for its intended purpose.
In /etc/NetworkManager/NetworkManager.conf , uncomment the dnsmasq option like so, because Network Manager's dnsmasq blocks listening to these ports if you want to run your own DNS server:
# dns=dnsmasq
But that's not all! We need /etc/resolv.conf to be updated with the external DNS providers that Network Manager discovers. This can be achieved by removing resolvconf which automatically alters /etc/resolv.conf.
apt-get remove resolvconf
There, done! Now add static configurations in /etc/networks/interfaces.d/ or /etc/networks/interfaces and let Network Manager handle your WLAN interfaces.