ECU power source?
 

Can I run the battery wire coming of my LS3 Speartech stand alone harness to a battery power terminal on my AAW fuse box, or does it need to go directly to the battery?

Your AAW fuse box has AUX plug. I think 6 circuits some switched and some full time 12v (assuming it's an update harness)

Pick up one of the ign switched 12v circuits and you'll have a fused connection from the AAW fuse box.

That is what I did. My Power Plus 20 harness has the auxillary plug like you had mentioned. The ignition and battery wires coming from the ECU already have their own fuses in line. The wires then run from the in line fuse panel to the AAW plug. I terminated the wires with a Packard 56 terminal and sodder and plugged them into the plug (which is also fused). Just wanted to make sure the ECU would be happy.

The AAW kits usually have a battery circuit for your ecu included.

It has battery/ignition circuits labeled for lighter, power windows, etc. That is what I used.

ECM Wiring
 

You should ALWAYS run ECM power and ground directly to the battery. Trust me here. The battery acts as a filter for transient noise, and you'll have way less voltage drop at the coils and injectors.

I am going to be using a battery kill switch mounted in the dash so I can reach it or the safety crew can reach it. I am going to run my ECU power wire to it. Wondering if I should run it to the in or out side for safety reasons. If I have it on the in side that always sees power, if I turn the switch to "off" will the motor still shut down?