First the USB port, nothing will happens if you plug your laptop to the USB ports, as it is ment to be the other way around as someone else here mentioned. You can plug the iPod, a USB memory stick or a USB harddrive. I use both memory stick and a usb harddrive on that port, but then again I have a diffrent headunit now, but as I read in the manual it works the same way on the stock headunit.
The 3.5mm minijack connection down with the cigarette lighter port is for auxillary audio input. You can use whatever audio-unit that has a sound output (preferably with line level). You can connect your laptop's audio output to this plug and hear the sound from your movie in the cars speakers
I have a CVT (it is like the AT without "steps" in the transmission) and I use the paddles for selecting gear when coasting down a hill. You'll save gas that way too. It works the same on the AT. I have found no other use for the paddles, it was fun to use only the first time. Probably gives you a better "racing feeling" using the paddles.
And NO you can not ruin the car using the paddles
Think of it: why would they make some buttons on the car that ruin the car when you use them? Would it not be better if the buttons where not there so no one accidental would use them...
All cars today is built almost idiot-proof, so goahead and play with all the buttons. You can use all the buttons on the car except popping the hood when in speed, THAT may ruin your car