If you have a "bad" cell, you'll need to replace the battery regardless.
If you have a cell with low voltage, and it happens all the time, an equalize charge should bring all the cells up to equally full capacity. The way a charger equalizes the cells is to apply a higher than normal voltage across the battery set. This will essentially over charge the fully charged cells, and bring up the undercharged cells to the same state. BTW, its important to use the manufacturer's specified voltage and duration to prevent damage.
Really there is no advantage to using a 6v charger on individual cells in a 12v set, unless you're trying to recover a particularly bad battery. If thats the case, you probably ought to just replace the battery set.
2000 Cherokee 29BH with 6V batteries, LED lights & 400 watts of solar power, flipped axles and raised. 2007 Tundra 5.7L DC-LB with lots of mods. C-co, 8/158th AVN Maint.