When you go through security you have to take out your laptop and put it in a separate bin to be scanned. So no, It doesn't matter what is in the bag.
No, Just put it in a zip lock baggie and you'll be fine. Just an FYI, all liquids must be less than 4 ounces, and be put in a plastic zip lock baggie.
fyi, they may ask you to turn on your laptop to show that it's an actual laptop. Putting it in sleep mode will make it go faster instead of waiting on it to boot all the way. The people behind you in line will appreciate it. Also, tape a card with your name on it to the bottom of it to help identify it so you don't pick up someone else's laptop at the security checkpoint by accident. The most important thing is to never let it out of your site.