This is much easier than you might expect
If you have two densities you can just subtract them and save the result in a NC file and visualize it in VNL. We do this in the I-V curve tutorial to plot the voltage drop: http://quantumwise.com/publications/tutorials/mini-tutorials/98
So, let's say you have the densities for A and B saved in files A.nc and B.nc, and we assume they are the only electron difference densities in these files, then a simple script will be the trick:
eddA = nlread("A.nc", ElectronDifferenceDensity)
eddB = nlread("B.nc", ElectronDifferenceDensity)
Then open difference.nc in VNL and plot it.