The charge equilibration function in ReaxFF uses the
current charges as a starting guess for each equilibration.
So setting the charges would only affect the first calculation
and make it a bit faster. In other words, it doesn't really
matter.
The charge equil is done over the entire system, So with
multiple molecules, presumaby they are close enough
to interact with each other, so the charges on all atoms
on all molecules are set simultaneously.
Steve