What is an algorithm for making a net neutral molecule from a set of guessed positive charges?
Although you did not mentioned specifically, it is likely that you want to perform some Molecular mechanics force field calculations. The charges are important quantity, so you need more than educated guess to obtain usable results. Nonetheless, the problem of charge equilibration is solved by "Polarizable force fields".

It should be noted, that they are often more expensive, less reliable and less accurate than standard FFs.