ok got a new 94' deville but..

its been sitting for 7 years, only got 65,000 on the dash and the 4.9 pushrod style motor.(thats the good news)
bad news is as follows, first of all this car has pass key and the person i bought it from didnt have the keys, so i go to the dealer with the title and get keys made. now when i get back the keys turn the ignition on but do not trigger the starter when i turn it to the start position, so i run a jumpercable to the batt. and jump the starter, she starts right up even after a 7year sit. i told the dealer about the key not starting the car he said they probally didnt program the resistor pellet in the key, but my whole prob is, isn't the pass key system suppose to disable the starter and the fuel pump??? if it is, then in theory the car should not run. also the alt. is not chargeing, so i got a new one, no charge still. so i run a 12 gauge wire from the alts remote wire on the alt's wire harness, to a ignition circut in the hood compartment fuse cluster (since it powers on with the ignition only) and presto, i got charge now.
so im actually driving this car around now, with the proper after sitting for 7yrs mantinence of course, and it drives great, so my 2nd ? is does the pass key dissable the alt as well as the starter , if any body can answer those two questions i'll be very greatful.
thanks Dre