I have installed nQuake which works awesomely with the basic Quake game, but I don't know how to link it in to the additional two Quake Mission Packs (Dissolution of Eternity and Scourge of Armageddon).
Any help appreciated.
nQuake is a package that was developed for online multiplayer in Quakeworld. Single-player compatibility wasn't really its intended use, so compatibility is likely to be poor with the mission packs.
I don't know what engines are commonly used for solo play these days, but maybe someone else here can suggest an alternative to ezQuake in nQuake.
Otherwise, try the site over at QuakeOne.com
, which is single-player community hub. I see they have a list of alternative engines in their sidebar.
nQuake (or ezQuake rather, which is the client in the nQuake package) can launch and run the mission packs, but eventually you'll get stuck due to some stuff not being supported and a door not opening or similar.
Install something like Quakespasm to get a nice faithful singleplayer experience with the mission packs.
Edit: when you have Quakespasm installed you can launch the mission packs by typing "game nameofthemissionpackfolder" in the console and then starting a singleplayer game via the menu iirc.