Use a special charger, such as an RV or boat charger, that has multiple outputs (best). Connect the two batteries in series, and use a 24V charger (ok, if the two batts are exactly the same). Connect the two batteries in parallel and use a standard 12V charger ( worst choice, one battery tends to hog the current, and they receive unequal charges). See the links for a dual-output charger I Googled.
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