What ran the battery down? were you using the radio for a long peroid of time without the car running?
Running the radio with the car running will NOT run down the battery unless the alternator is bad.
GM recommends running the radio leads to the battery with fuses at the battery. Go to this web site for more information from GM:http://service.gm.com:8083/techlineinfo/radio.html
Car starting batteries do not like to be drained down and then recharged. If you are using your system in that fashion, I would suggest you put in a second battery in your car that is a deep cycle battery and use it just for the radio. This way, you can use the radio with the car off and not worry about draining down the main battery.
If the radio was not being used except only when the car was running, then you have other problems with your electrical. A 50 watt radio at 12 volts will pull about 12 amps Max. and your alternator is rated at about 95 amp output. So you see, your alternator should not have any problems keeping the battery charged.
I hope this helps in your quest.