That extra bat you have in the trunk will help to protect it some but Essentially your alt still has to recharge them both after the charge is released. Look into estatic bat caps. They are high performance car audio batteries but they charge and release energy as fast as a capacitor putting a lot less strain on your alt because it recharges much faster and more efficiently than a battery, even other car audio batteries. The best thing you can do is a alt upgrade. Our alt is only 110amps. The car requires 50-60amps to run properly and efficiently, especially since our cars are so electronically managed and throttled now. That leaves you with let's say 50 amps just to be safe. Even the jl 500/1 with it's state of the art regulated power supply that is patented by jl uses 54amps. The 1000 watt jl pulls right at 90amps. This should give you a perspective. And I didnt have a second amp for mids and highs. That is probably pulling another 20-30 amps. Trust me from experience with my previous vehicle, it will damage more than just your alt by doing this prolonged. It will actually ruin the engine management system of the car[?|]I think I'm going to start to have alternator problems all thought I havent yet and I've had this exact same system for 5 months or so...I dont even have the heat extractor on the alternator anymore I did however do the big 3 so I'm sure that's helping my volts are running 13.7 13.8.