You can get a plug-and-play harness for the MSD box. It's been years, but I believe it has six wires: Positive and negative leads that go to the battery terminals (or negative to chassis or engine ground), two that connect to the ignition coil wires from the vehicle harness, and two that connect to the ignition coil, where those harness wires originally went to. It basically splices inline.
*EDIT*
I had to look it up and found this:
The adapter harness so you don't have to cut your factory wiring is around $40. Personally, I'd sell the MSD box before cutting the factory wiring or investing money in the harness. The MSD will make no measurable gain in performance and will burn up the terminals in the distributor much faster. If anything for ignition, I'd put the money towards new OEM components.