Total noob question.
I found the wad files for the master levels in my gog folder, but I noticed that the wads are arranged differently than they are for Doom and Doom II. Is there a way to put all of the master levels in GZ Doom together as an entire "episode", or are they more meant to be played by themselves pistol starting each level?

If you have all the Master level Wads, and the original Doom and Doom II wads, and the Final Doom wads (TnT, the other one) you can use wadsmoosh to put them all in one single PWad. You can include the extra Doom II add on No Rest for the Living from... Doom III I think? And Romero's Sigil episode as well if you those Wads.

https://jp.itch.io/wadsmoosh

I would say to use the Master Levels Menu Interface mod, as this gives a menu system to select the level to play, just like the original DOS release has, as the Master Levels aren't meant to be played as a single campaign with all the levels back-to-back. Each one is meant to be played separately, from a pistol start.

Below is the link to the Master Levels Menu Interface, but some setup is required.

https://forum.zdoom.org/viewtopic.php?t=20795