If you do want to use aftermarket LP-E6 batteries in your factory charger, they MUST have a facsimile of the Canon chip in the battery, otherwise the factory charger won't work.
I buy some aftermarket batteries straight from a small factory in Sydney, and they do put a copy of the Canon chip in the packs, and they work just like OEM Canon batteries.
If your battery pack does not have the correct chip in it, the factory charger that comes with the 5D3 or newer cameras just won't work at all, and may actually end up flattening your aftermarket battery.
However, if you have non-chipped batteries, just buy an aftermarket charger.
Many of the cheap Chinese web sites selling copy LP-E6 batteries actually supply an AC charger with each battery because they won't work with the newer Canon chargers.
Even the non-chipped batteries will work in your 5D3 or 6D etc., but you might not get accurate, indeed any, battery monitoring.