I had a long, long talk with Mark from Mad Elec about six months ago and have since then really studied this issue. The best possible spot to connect is the positive stud on the starter relay. The idea is to establish a power point that is between both power sources. The attached drawing Mark asked me to draw explains it a little better than my text here. Power moves in the direction of the draw. When the alternator is running power goes TO the battery, when the power is off, it comes from the battery, etc. Basic stuff I know.

In short, the primary power distribution point right now is the welded wires under the dash. The idea is to move that point inside the engine compartment so the primary power does not have to cross the bulkhead connectors. Unless you establish a new "central" point, the best default one is the positive stud on the starter relay.

This new power point should then be the primary tap for things like headlight relays, fans, etc. If you look at the arrows in the drawing you will see that when the alternator is running, ALL power to this point will be pulled from the new central point. However, this only reduces risk if you run a jumper between the ALT and the positive stud. One or the other won't help you much.

To really make a difference, you need to:

1) Run a Bypass wire
2) Move the "central" power point from the weld to something like the positive stud on the starter relay.
3) Begin placing relays in the engine compartment for lights, fans, etc.

I have done this and it looks invisible and made a huge difference to my power. I can send plenty of photos but they are all from an E-Body.

-Steve