With my experience of using DNSCrypt I actually think that Qubes' has some 
unique way of handling DNS queries given how the nameservers automatically put 
into /etc/resolv.conf are on a different subnet.

I actually think there must be some sort of bind or unbound being ran in there 
that resolves all the DNS queries for you by using sys-net or your netvm as a 
proxy.

In order to make a sys-dns qube or to turn any other qube into a sys-dns qube 
you must ensure that it is listening on port 53 UDP for any DNS queries.

This command alone given by Chris should be enough.
iptables -I INPUT -p udp --dport 53 -j ACCEPT

Afterwards you should change your /etc/resolv.conf to the IP address of your 
sys-dns qube. The IP address can be found out using Qubes Manager and try to 
ping that ip address first to verify if it is reachable by your AppVM in the 
first place.

If your sys-dns qube is not your sys-net or netvm then you should ensure that 
TCP port 853 outbound is allowed through if your firewall rules do not 
explicitly allow all outbound (all outbound is allowed by default for each qube)

(In dom0 terminal)
qvm-firewall [sys-firewall or/and sys-dns] add action=accept proto=tcp 
dstports=853 --before 0

If this doesn't solve it then it may be best to provide us with some logs of 
your stubby

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