Electrical Questions / Wiring

... run a secondary wire from the alternator to the amp itself to power it off the alt not the battery? ...
The alternator output stud is already wired direct to BATT+. In the factory, it routes thru the dash ammeter. After the MAD Bypass, it will be exactly direct.

You don't want to use BATT+ (or ALT+) directly to the amp (unless it has an on/off switch) since those are "always live" so the amp will draw down the battery overnight. You should power the amp via a relay. Actuate the relay's coil by the ACC wire (under-dash) so it turns on with the key. You can't use a standard 40A automotive relay. Maybe need a "solenoid" like the external starter one on 1960's Fords, if your amp as bad as you state. But, read the amp manual for direction.