It's been a while since I tested the VSPAERO GUI for reversing propeller directions or manually setting the rotation. If you look at the Prop in Blade mode, the default is to turn 'right-handed' or clockwise viewed from behind. The Rev flag under Design will reverse the blade geometry to a counterclockwise rotation. Now the Disk mode, for some reason that I've forgotten to talk to Rob about (my bad), has the _indicated_ direction reversed from the Prop direction. I think it has to do with the rotation being about the X-axis where positive follows the right-hand rule (counterclockwise) but the arrow indicating turn wasn't updated to reflect that. Justin Gravett made it so the GUI will automatically set the proper turning direction in the VSPAERO input file regardless of the indicated direction so you don't have to set a negative RPM in Disk mode vs Prop. So VSPAERO will see rotors turning in the direction indicated by Blade mode, regardless of what the disk direction shows. Run a simple VSPAERO case with a disk and wing to see for yourself.
That's a long way of saying, just click the Rev button. And, yes, you are very likely going to see a difference.
The .bem file uses the Prop wireframe to set the sections. So Num_W (chordwise) will set how many airfoil points are written and Num_U sets how many stations. Twelve is the default Num_U.