Smells like a wires burning

Today I went out to start my car and let it run for a little bit and the battery was dead. I tried to jump start it with my pops car and when I hooked the jumper cables to my car I heard this noise of something running, that I've never heard before while hooking up. Few mins after charging the jumper cable starts smoking on my battery. My reaction to that was take it off fast.. so I did. Went to give it a shot and try starting. When I got in the car is smelled like a wire got too hot, or burned. I'm hoping im lucky and its nothing..

The smoke from the smoking battery terminal could not have gotten inside the car that fast, or anyway. As soon as I seen it I took it off.

postive to postive and negative to negative... I finally got my car started and theres a couple things that dont work.. Kinda odd too...

My remote doesnt work to unlock or lock or pop open the trunk, my power door locks lock, but don't unlock. My radio doesnt turn on nor the cd player, but whats odd about that is when I hooked up my pillar gauges i ran it off the radio power wire and the gauge still works so theres power still there somehow. my 12v acc still works. windows still roll down. When i got my car started it was a jumpy idle.. it was like vroooom vrooom vrooom like up and down.. Its never done that before, but I figured it was the cold weather and that I didnt start it after a couple days.