Does anyone know anything that would make map-making, or at least organizing a map easier than on paper (the eraser marks eventually make parts unusable after a while)?

You just want a computerized tool that will allow you to draw boxes and connections?

If so try Visio or Dia.

I use autorealm - I can’t remember the url offhand, but you can find it easy enough on google. It’s an open-source rpg mapper, which can do anything from very simple block diagrams to full on terrain maps.
I like it because it allows me to do a little more than a simple block diagram - e.g. approximate room sizes and shapes, locations of key objects, puzzles etc.

I use the Infomer IDE for my Inform coding, and it comes with an automated mapper, which you simply feed a transcript into to get a map. Unfortunately, Informer is hard to find. Good luck.

I use IFMapper it does everything I want it to and no need for paper!