If the batteries are of the same type (both flooded lead acid or both AGM) then size doesn't really matter for your application. How the battery charges is going to be primarily a function of the overall condition/age of the battery. Unfortunately, calendar days is not a good way of measuring the age of a battery. If your stereo battery gets deep cycled a lot then it will age a lot faster than the starting battery. If you are using the batteries independantly (starting on one, running the stereo off the other) then you will be able to tell when one of the batteries is going bad and thus the age/condition issue is minor. On the other hand, if you were permanently connecting two batteries in parallel and using them as one unit then it is really important that the two batteries be as matched as possible: size, age and manufacturer.
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