At the risk of revealing my ignorance, I have a couple of questions:
1) e36s came with three alternators, 80 AMP, 120 AMP, and 140 AMP. Which are you using?
2) You mentioned that the cap on your amplifier was 3000 watts. How big is your amplifier?
3) Are you using stock headlights, and do you drive with your running lights on? If you have all those things turned on at once, you are going to have a problem, but the biggest loads will be the audio amp and the headlights.
When you count up your load, remember that each headlight is 55 watts (at least) on low beam, so with driving lights we have 220 watts up front. Toss in another half dozen 15 watt running lights and we are up to 310 watts (24 amps) constant load when you flip on the headlights. Toss in another 8 amps for the ignition and computers, and we are up to 32 amps before you turn on any toys.
Two batteries will help only if you have a light-dimming sudden load that fries the alternator. If the problem is exceeding the alternator's duty cycle and overheating it, all you can do is adapt a bigger alternator and try to keep it cool.
There were 5-series police cars in the 1990s. I doubt that those alternators are still available, and if they are, only European vendors would carry them.