I use wpa_supplicant + dhcpcd directly for Wifi. My internal network is usually configured statically from rc.d scripts or even systemd-networkd.

I don't like when dhcpcd mess with my DNS, so I usually use a static resolv.conf pointing at my own DNS.
For the VPNs, I handle them as normal daemons (they modify my resolv.conf though).

I know that this might sound boring, but once all this is setup, you don't touch it again :)