How do subscripts represent the charge balance of ions?

They don't. Charge is normally denoted in superscript.

While Capuchin is correct that charge is denoted by the superscript, it is also true that adding ions can change the charge. For example, CO3(-2), carbonate has two negative charges. If you add one hydrogen ion to it you'll get bicarbonate HCO3(-) with only one negative charge and if you add a second hydrogen ion (H+), you'll have H2CO3 and there will be no charge on the molecule.

Note that if you have CO3(-2), you must have something that represents the associated positive charge (two Na(+), for example). Ions don't exist alone.