Do I score the area number per disc and cube that is in the area, plus bonus point per cube that is in same city as disc?
Yes, assuming you're ignoring every piece that is not your color.
I read the score correction on Rahdo runthrough and that reads that you receive (in area 2)....2 points per disc.....2 points per cube in same city as disc and a bonus point for each cube in same city as disc.
Each of your cubes scores 2 points (in area 2) regardless of discs in the same location. Then you also get the bonus.
Here's how I think of it: Each of your cubes and discs gets points equal to the area number. In addition, for each location, multiply the number of disc you have (in that location) by the number of cubes you have (in that location) and score it as a bonus.