1995 Volkswagen Passat 1995 Volkswagen Passat vr6 will not

I have a 1995 volkswagen passat car, it is a automatic vr6 cylinder engine. My problem is I bought this car from someone which he had the car sitting up a while and decided to sell it. When I purchased the car it had no motor in it but he had a motor he bought from a junk yard and included it with the sell of the car. I installed the engine and hooked up everything which I think is correct because the engine still had all the hoses and vacum lines still attached to it, and the car had the hoses and lines still on it so all I did was to match up them and connect the electrical wires. The wires could only be connected one way because the connectors will only fit to the one it is suppose to. What I am not sure of is where does the large wire coming from the altinator hook up to. I figured it was suppose to hook up on the starter motor with the battery positive cable wire. Is this correct?
the car will not fire up when I turn the car ignition switch, it will not do anything. So I hot jumped the starter directly up to the battery and the starter worked, so I ruled out a bad starter. But even when I done this the car still would not start it would not fire at all.
any suggestions on what could be wrong with the car. I need to know why car would not turn over when I turned the key unless I hot jumped it, and why car will not fire when I hot jumped car by directly hooking up to battery.