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The only concern is the current draw- unless you manage to run both batteries dead flat you won't have a problem.
Look at the fuse ratings for the amps you run. Figure your car needs a good 10-15 amps just to run, then add 10A for headlights, 10A when you run the blower, 15A when you run the defrost, and so on. Charging can draw just a few or 10's depending on how low it is.
Anyhow- you should always budget as if you don't have a battery, except for the charge current. Generally speaking, when you have a big system, you need a big alternator to keep up with it. What usually happens is you start frying alternators. There is no way for an alternator to limit it's output, so when you draw too much... you just stress it and can damage it.
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