Best way to rewire for an MSD?

So I've been having trouble getting my stock electronic ignition to run right with my new engine set up so I borrowed a friends MSD unit and it fixed all most of my issues. My question is what's the best way to wire an MSD bypassing the stock wiring harness. When I hook my friends unit I hook the Coil lead to the ballast wire. But I couldn't start the car with the ignition key. I ended up starting from under the hood and car ran fine. I'd like to know the best way to bypass the factory wiring haness, maybe eliminated it completely. Any suggestions?