alternators don't generally have a negative they normally ground through the body to the block, it's imposible for me to say without pics, but if there is only one wire out of the supresor then that would go to the +ve output of the alternator the thick wire and the supressor would bolt to the alternator
but if you're hearing the engine through the speakers it's more likely you have a seperate fault as most alternators i've seen e.g the bosch ones on a cossie , have a suppressor already on, although i supose this could have become open-circuit.
did the stereo ever work properly or have you just fitted it?
mind you if that one cures the fault then end of problem...
other thing you might wanna do is check all your earths e.g. battery to shell etc
let us know how you get on, pics wouldhelp