Our battery kits do not require the alteration of any factory circuits. You may get a useful recommendation from the battery manufacturer though, so feel free to contact Optima or Odyssey directly to discuss charging requirements for their batteries.
We agree with battery manufacturer guidance that says the alternator is not a battery charger, and should not be expected to perform as such. If you have a discharged battery, their recommendation is to use a battery charger to recharge the battery properly, not the vehicle's alternator.