I am installing a upgrade wiring harness for a 1967 mustang. What is the best way of doing it.?

I bought a upgrade for my 1967 mustang wiring harness from American autowire. There are a lot more wires than the original wiring harness. I was wondering before i get started what is the best way of doing it. Is there anything i should look out for. Is there anything i shouldnt do.

I also need to get connectors. Where is the best place.

Harness looks like this:

http://image.mustangmonthly.com/f/17975049/mump_09...

If anybody has done this before i am open to your tips and suggestions.