The cable with the cover is the positive starter lead. On my car, it runs right into a junction the previous owner made out of a battery terminal.
The black with white wire also leads off the starter, but I'm not all sure where it goes before it hits that little starter bundle again.
The other 2 wires are connected to the alternator, then into the starter bundle, and that goes to the body harness, on my car. It doesn't look like he messed with that set of wires, so I assume this is the stock layout.
When I have my terminals connected to a good battery, my car cranks just fine, but the ignition harness, among other bits of the engine harness, was bad (SEv6 ignitor on a CA-DET, what?), so it doesn't turn over.
An image to point things out: (taken, leaning over the passenger strut tower, looking between it and the intake manifold.)
(Mind the butt-end splice and the missing bolts. They were like that when I bought the car)