Typically the standard system has two coil wires: the first is for starting, usually yellow, and comes from the ignition switch IGN2 terminal on "A" bodies, OR the "R" terminal on the starter solenoid for "F" bodies. THe wire for power when running is a resistance wire that ultimately comes from the IGN1 terminal on the ignition switch. For HEI use, bypass the resistance wire with a 12 Ga. wire; leave the yellow wire where it is, i.e. the two wires come together at the HEI BAT terminal.
You can't use the alternator output wire, it has battery voltage all the time. If you connect to that, your ignition will be on all the time; really bad for gas mileage
Geo