Actually, to me it may mean that whoever the installer was, they took the lazy route when they wired in the harness and instead of creating a dedicated standalone circuit for the sound system, they may have piggy backed it onto an existing harness, either by using those blue guillotine wire connectors, or by physically stripping a small section of the wire, wrapping the parasite feeder wire around it. and then just taping the whole thing to insulate it. I have even seen masking tape used as an insulator!!
Even with the stronger alternator, the circuit that was co-opted as the source of power is only as strong as what it initially fed power to. If you were getting voltus interruptus then a circuit breaker somewhere may have been added that killed the power momentarily and then reset it once the wires cooled down again. Don't count on that; it could just easily be a sloppy/loose wire marriage of the parasite power wire to the source power wire that was making and breaking itself due to vibration or interaction with an adjacent piece of infrastructure. Don't think it was the new alternator that solved the problem, although your battery may have been thankful.
The mark of a reputable and experienced sound system technician is the work and thought they put into the wiring, sizing it correctly to meet the demand, the routing needed to avoid other components, the type of connections, and generally the overall fit and finish of the system. From such an individual you would get a sub-circuit exclusively dedicated to powering your sound system, with relays and breakers to protect the components from power surge or damage, and with heavy gauge wiring--think 10 ga primary wire as the absolute minimum here, more probably to be 8, or even 6 or 4--for the power feeds from the distribution board and a battery sized power wire to feed it. Depending on the system specs, there may even be a memory wire that goes to the receiver because any cpu's that are in the system need continuous power from an outside source or they lose their "minds".
As to how to go about doing a wiring circuit witch hunt, Just start with the battery connections at the battery, and follow them. That big red wire will, eventually and one way or another, take you to every other circuit in the whole car. To do the job properly you will need that probe that I posted the picture of earlier as well as a good multi-meter, some jumper wires, and a SH*T-TON of patience. Expect to get dirty and bring along an old toothbrush as you can use it to gently brush the crap and crud off some of the connections so that you can get a better look at them. Don't be afraid to physically touch and gently wiggle things; you be surprised how much information you can get from your finger tips.
Good Luck and Good Hunting.
Nick