Newbie needs BIG help on stereo set up

[Witz352]

Newbie here..........it would be awesome if someone could help me out. I have a 2000 seadoo challenger 20ft with a mercury v6 2 stroke 240hp. I've recently installed two subs and some tower speakers. But after the fact I'm finding out that my engine only puts out 40amps to the battery. I have an extra battery and capacitor that the stereo runs off but its connected to the main battery. Is there something else I need to make this work? I have already burnt up my rectifiers once and I'm trying to avoid doing it again. Thanks