I’ve spent a lot of time talking about encounter tables. Like, two Earth months. So at the risk of prattling on even more about stuff you will doubtless figure out for yourselves, let’s move on to actually lighting this candle.
What We’re Doing
Yeah, I had to go back and check, too. The goal is to create a mini-campaign with a random map populated via random encounter tables. We’ve got the map, and plenty of encounter table advice, but true to my form, I need to throw in a couple more details.
First off (and I didn’t specify before), this will be a fantasy setting. I’m currently reading The Coming of Conan the Cimmerian[affiliate link], so I'm gonna steer in that direction. 
Second, I had decided that the sub-tropical island of Minocra is ripe for colonisation, so straight off, adventures will be carving out territory, protecting soft settlers, responding to threats, and exploring scary places. I have no details yet, but going forward, I absolutely will be connecting back to these dots.
You’ll recall that I used MapGen2 to create the map. The author of this handy tool is Amit Patel, who created a terrain key for MapGen2 output.
However, I'm going to take a few liberties, as the map provides a good visual—you can easily see that brown areas are more arid, green areas are foresty, and grey/white areas are probably mountains. For better terrain definition, I suggest the Biomes view in the MapGen2 tool. 
Here’s a suggested terrain key you can use for all climates:
Even though I plan to use random encounter tables to describe and populate the setting, it makes sense to create a few fixed locations to act as "hubs" of activity. Settlements, important ruins, and known places of dread need to be rooted, if for no other reason than to assure the PCs that there are some constants in the setting.
I'll go random with these fixed points, using the guidelines in part 2 of Hex-based Campaign Design, but only for Major encounters.  This means I'm going to roll a percentile die for each Atlas hex and compare the result to the hex's "primary" terrain (on a hex map, this is would be the centre hex, but in this case, I'll define it by whatever terrain type is most abundant). Also, because I'm in a sub-tropical clime, I'll apply +5% to each roll.
Consolidating half-hexes on my Minocra map, that's 30 rolls. There are 22 full Atlas hexes on the map, plus 16 half-hexes. I’ll roll individually for each Atlas hex, but because the half-hexes are predominately ocean terrain, I’ll simply make 8 rolls to cover them all and distribute the results where they look pretty. Here's what I ended up with:
I rolled really low on my percentiles, so much so that 17 of my 30 Atlas hexes contain a fixed encounter.  The results, straight from the table, are shown above. The next step is to shape these results just a bit and fix their locations.
I count this as progress. The random table for fixed encounters did exactly what I wanted, which was to give me idea starters. Looking at these en masse, and coupled with the Conan vibe, I can start to ask important questions. Like, why so many ruins? What was that disease and did it force the migrations? Who's in those jungle fortresses? What’s a Lawful religious ordering doing in the rain forest, and what’s up with that settlement in the ocean?
The setting is starting to take shape.
But it doesn't show elevation, so use the 2D Slopes view for that.
Ah, but what about Minor encounters you ask? You'll see, kids. You'll see.
These are legitimate rolls. I was tempted to fudge one of them, but I didn’t, so what you’re seeing is straight-up results, unblemished with the taint of bias. If dice wore chastity belts, my polyhedrals would still be virgins.