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If you follow the advise posted by Richard, there is no possibility of 'hurting' anything on the 6V side of the car. The ONLY thing that sees 12V, is the starter, if done this way. Problem is, many people don't understand this, and simply hook 12V across the 6V bat. For this scenario, usually nothing bad happens, but there is always the possibility that 12V can hurt the ignition system, or anything else that is turned on.
I choose to stick with Richard's way, noting that there must be at least enough 6V available to run the ignition (since it doesn't get 12V using this method).