Aside for grouping Basic Actions together you should group:
- Melee Attacks
- Ranged Attacks
- Social Actions
- Spells
- Prayers
This way, when someone wants to create a melee oriented character with a dose of social interaction, he will only have to look through potentialy interesting cards. You can easily tell these categories by the nifty icon in the upper left corner, and there isn't really all that much of them in the first three categories.
Additionally, you should separate the spells and prayers by order and religion respectively, again putting the basic cards available to all wizards/priests aside, and sorting the other cards by rank. This way, when someone creates a new wizard/priest, he can easily see what actions are accessible to him immiedietly.
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.
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I print off custom maps from map creators, then lay an acrylic sheet over top. The hard surface is easier to place minis on and you can use dry-erase markers to augment the map with traps, AoE effects, etc.
To add Fog of War to this setup, I use butcher paper in between the map and the acrylic then slid it out as the players progress. I have also used overlay map pieces (from the map creators) to hide portions of the maps (a roof for the hut, cave rock texture, etc.). From the player's point of view, they see a large map with a full-colour map texture but no paths or rooms or interiors. These pockets get 'revealed' as they get in range. It has worked well for my games.