A megadungeon is simply too large to feasibly represent during play at 1in=5ft scale, even if you were wanting to, without a lot of work. I find that drawing out every section either beforehand or during play in battle-map scale is a lot of work for very little value. It's more effective to save miniature-scale maps for where they are most effective.
So instead, represent only the sections where combat actually happens, and during the exploration segments of play rely on just description to convey the layout, keeping your large-scale DM's map only as a private reference. That description-only information preserves the sense of exploration and uncertainty, allowing the players to use/need their smarts to figure out layout secrets, and maintaining the possibility of the PCs getting legitimately lost (as opposed to the kind of "story says you get lost now" approach that doesn't suit a megadungeon).
You can do this two ways. You can have "combat arenas" prepared in miniature scale in as much detail as you want, and lay those down when combat is either already broken out, or when it's obviously imminent even if initiative isn't yet rolled. The upside is you can put a lot of detail into these set-piece maps, but with the downside that for your prepared areas to be predictable, you have to build your whole megadungeon to neatly divide up into predictable combat arenas.
The second way is to draw out the map on the fly when combat occurs, on a vinyl battle-mat or small sheets side-by-side, using your master map for basic layout and your notes for room features that are relevant to an exciting combat. The upside is lots of flexibility in handling combats wherever and whenever they break out and go to, but the downside is that the maps won't be nearly as pretty.
You can also mix and match these methods. Say you decide to draw everything out, but you find an excellent ruined cult sanctuary tileset and want to use them—nothing is stopping you from busting out detailed tiles for one or more special rooms in the dungeon. Similarly, you can prepare all your combat-area maps beforehand in gorgeous detail, but fall back on sketching rooms and halls on a vinyl mat when combats occur in unexpected places or if they overflow outside of the prepared areas.
The thing these share in common is that you don't show your players perfect, miniature-scale maps for every foot of the dungeon, only "zoom in" when combat happens. That keeps the rest of the exploration in the mind's eye, where inexact knowledge of the layout can keep the "megadungeon mystique" alive for your players so it can enrich their experience of the place.
D&D 5e does not need a battlemap ... but you knew that already, right?
However, to take it further, a bettlemap adds to D&D 5e for close range (melee) combat but adds next to nothing for long range combat. Unless and until the combat reaches a range where melee combat is a possibility, just do without the map until that happens.
Instead, keep track of how far the groups are from each other until the range closes. You can do this precisely if you like or, for normal movement creatures (20-40 feet) if you just keep track of how far apart they are in 30 foot increments and each time a group uses movement (or Dashes) to close the distance, reduce the range by 30 feet. In general, most groups will want to stay in support distance of each other so they will move at the speed of their slowest member. If some do want to dash ahead or stay behind, just break up the group into as many as you need.
If you like, you can get each side to set themselves up 6 squares apart in the relative positions they want and write the range between them, when it reaches 0 they are in melee range and use the map normally.
Best Answer
You don't exactly need plugins for this sort of thing: the most important skill for using raster software like the GIMP for map-making is learning how to use the existing functionality to get the effects you're interested in. However, depending on what you're going for, there are plugins that can help.
The hardest part of making a fantasy city map is laying down the streets—everything else (city walls, surrounding terrain, water, building fill, text, etc.) is the application of more basic cartography techniques. If you've got a small city or are drawing only a high-level view of it you can get away with hand-drawn streets, but for more complex streets like in this city map that would be mind-meltingly tedious.
If you're on Windows using the GIMP, there is a Voronoi diagram plugin binary that can randomly generate street-like lines (as seen here) suitable for a city map, but it's an old plugin that isn't maintained anymore. I haven't been able to find any others, though.
Another method is to use something other than a plugin to generate a network of lines: this tutorial uses a city-generating program to create a street network image, which is then imported as an image and traced by hand. Another sources of "street-like images" you can trace is stock photography of broken glass.
For a less street-dense map, working on improving your map-centric image manipulation skills has more payoff for the time invested than experimenting with plugins to do the job. This tutorial on creating fantasy city maps at the Cartographers' Guild is an excellent place to start even if it is written with Photoshop in mind.
Finally, the unquestionably-best way to learn how to create fantasy city maps in GIMP (if you haven't already guessed from the festival of links) is to sign up at the Cartographers' Guild forum so you can read through the reams of material there. Try a search for "city streets" for pages of discussion and pro-looking maps to get an idea of what's out there.