Lost editing DNS config in Ubuntu 18.04

Objective

For personal use, I need to add a custom server running on 127.0.0.1#5354 that resolves queries for .hyperboria domains.

What I've done

There used to be a file called /etc/resolv.conf that now says,

#     DO NOT EDIT THIS FILE BY HAND -- YOUR CHANGES WILL BE OVERWRITTEN
# 127.0.0.53 is the systemd-resolved stub resolver.

So, it seems that since systemd is the main responsible for everything, I should look into systemd-resolved service/configuration.

I could just edit the NetworkManager WiFi settings in GNOME to add a manual DNS server on my connected network, but that doesn't apply for every network (just the one I've edited). Plus, I couldn't control which domains solve with each server, and I don't know which files are being edited behind the scenes.

On dnsmasq I think I could just add this line to its config, server=/hyperboria/127.0.0.1#5354, but dnsmasq is not running, and if it would, I've found out that it is wrapped by NetworkManager or something similar and I wouldn't know if I should add a file into /etc/NetworkManager/dnsmasq.d/ or edit /etc/dnsmasq.conf.

Other possible configurations are,

• /etc/network/interfaces # not sure how legacy it is these days
• /etc/resolvconf/resolv.conf.d/base|head|tail

Anyway, everything seems to rely on systemd-resolved. How could achieve this?