If you already have cube files of electron density for dimer, water1 and water2, you should calculate cube file of electron density difference (EDD) based on the three cube files via grid data mathematical operation in main function 13, see Section 4.13.2 of Multiwfn manual for example. After that, set "iuserfunc" in settings.ini to -1 or -3 (corresponding to three-dimensional trilinear interpolation and B-spline interpolation based on the grid data in memory, respectively, see Section 2.7 of manual for more information), then boot up Multiwfn and load the EDD cube file, use main function 4 to plot contour line map in usual way and choose "100 User-defined function" as the function to be plotted.

I tried to plot the density difference contour between a SCF converged water dimer and the two separate water molecules. Following your example 4.5.5 in the manual, I was able to generate the desired 2D contour plot using water-dimer.fchk - water1.fchk - water2.fchk. However, when I tried with cube file input, I couldn't get any 2D contour result. I also tried to generate the cube file with difference density, but after choosing plot planes, I got

4
-10 Return to main menu
-2 Obtain of deformation property
-1 Obtain of promolecule property
0 Set custom operation
             ----------- Avaliable real space functions -----------
1 Promolecular electron density
8 Electrostatic potential from nuclear charges
14 Reduced density gradient (RDG) with promolecular approximation
16 Sign(lambda2)*rho with promolecular approximation
22 Delta_g (promol. approx.)
100 User-defined real space function, iuserfunc=  0
1

and the plotted 2D contour is that of water dimer instead of difference density. Is this function simply not available with cube type files? If it supports cube files, what should I do to print 2D contour? Thank you.