CD player stopped working on 99 Sonata

I have a '99 Hyundai Sonata. I lost my keys recently to my car so I had to use a spare. My car is equipped w/anti-theft security alarm, so when I opened the car door w/my spare key, the alarm went off and it locked my ignition, therefore I couldn't start the car which would have turned off the alarm noise. My only option was to disconnect the cables on the battery. When I found my original keys w/the remote the next day, I reattached the cables to the battery which sounded the alarm again but this time I turned it off w/the remote, I also had to jump the battery because the car wouldn't start after I connected the cables back onto the battery. My problem is my cd player/radio/tape player was working fine until I had to disconnect cables and have my battery jumped. I need help ASAP! Thanks, daley61