Navigate to Core/LUA/GFOW_FogScript.lua. Open it with notepad, but I recommend using Notepad++, or Sublime Text.

These are the things you can change:
1) Base Number of plots to fog (int)
2) Radius around the city to keep uncovered (int)
3) Radius around the forts to keep uncovered (int)
4) Whether friendly forts block fog (true/false)
5) Should discovered resource icons be hidden (true/false)

6) Probability to fog before Optics (float)
7) Probability to fog after Optics (float)
8) Probability to fog after Compass (float)
9) Probability to fog after Astronomy (float)
10) Probability to fog after Navigation (float)
11) Probability to fog after Flight (float)
12) Probability to fog after Radar (float)
13) Probability to fog after Satellites (float)

Note: Using these probabilities you can change when you want to the fog to stop growing.

14) Whether to fog a Mountain (true/false)
15) Whether to fog a Barbarian Camp (true/false)
16) Whether to fog an Ancient Ruin (true/false)
17) Whether to fog a Resource (true/false)
18) Whether to fog a Coastal tile (true/false)
19) Whether to fog a Ocean tile (true/false)

20) Which takes priority, Terrain or Resource (true/false)
21) Should fog be connected (true/false)
22) Whether Great Wall should fog the civ (true/false)
23) Whether Great Firewall should fog the civ (true/false)
24) Does Wall reduce distance of uncovered tiles (true/false)
25) Does Castle reduce distance of uncovered tiles (true/false)
26) Does Arsenal reduce distance of uncovered tiles (true/false)
27) Does Military Base reduce distance of uncovered tiles (true/false)

It took me a long time to implement all of these settings, but in the end, I think it was worth it because now the user has choice to change things to what he likes. Don't be afraid to experiment, and also if you have suggestions for more settings, please comment.