I have run both the MSD 6AL and the Crane Cams HI-6 in the way I described (can't remember the colour of the wiring, it's been a while since I have done one). Let me try and explain this in a way that doesn't sound to confusing.
You are making the same mistake I did when first trying to wire one up to the Holden V8 EFI system. Tried to over complicate the wiring.
The 6AL will only work in increasing spark. Timing is still done through the computer/ignition module. If you try to run it through the 6AL, you'll probably end up with a mess of wiring and a car that won't start.
So essentially power that usually goes to the coil, now goes to the 6AL, it increases the power there, which sends it to the new coil. Spark timing is still done through factory means. All you have done is re-route and increased power going to the coil.