I left the encounters how they are. I'm using them to generate general threats in the area, not tied to specific coordinates (for the most part: I do use the ruins and boss monsters, just re-interpret for the setting). I changed the encounter and luxury sprites into various run down buildings (I used SNES sprites). I'm treating those icons as rumors, "Your character heard about 'x' at that place" - so they're all visible to the players at the start. I'll be using additional generators to then fill out the maps with "secrets" to find.
I'm using all the kingdoms to represent settlements and stuff. It's super helpful. By using your program I've easily avoided like 40 hours of game prep, at least. And it's also a lot of fun to use! If you're curious, this is the map your program generated for me https://imgur.com/a/ITuE7Cb. I hope you don't mind that I'm using it this way. I rarely comment on stuff, but Sandbox World Generator is by far one of the most useful pieces of software for campaign prep that I've encountered. I'm running a "west marches" styled game for people online, and the map this outputs is fantastic!