Talk to me about biking and commuting

I have commuted all school year and have only driven a handful of times. Even in freezing and rainy conditions. First off, I ride my MTB for the commute(only live 2 miles from work). Second, headlight system and red flashing lights. Third, reflective vest. Fourth, assume every car is going to hit you. And last but not least, do not put banans in the same section of your backpack as apples or oranges.
Don't let the short distance commute fool you. I get my long rides in after work and take a route to some sweet trails and ride off-road for a couple of hours before going home.

I have never had problems in the dark, probably because there are few cars; but there can be lots of problems if you try to commute during rush hour. People are in a hurry and don't pay attention to you, or they take greater risks when passing you, etc.

The only things you can do to be safe are follow the rules of the road and make yourself as visible as possible. Ultimately you have no control over whether someone hits you or not, but if you act predictably you'll be much less likely to be in an accident. On the other hand, if you're running red lights and hopping on and off the sidewalk as is convenient, you expose yourself to more risk in addition to inciting drivers against you. If you're on a bike, pretend you're a car.

Acting predictably will also make you more visible, but you should also put a bunch of lights and reflective gear on. Blinking lights attract more attention than steady ones. You might also consider wearing a yellow jacket or helmet cover, because those stand out. Yellow clothes are especially helpful when it's light enough that your wimpy bike lights don't show up well, but still dark enough that people can miss you.

Oh yeah, bring a cell phone with you too.

If you are going to commute in the early morning hours when light is low, get yourself a head light.  Or, at the very least some flashing lights; they only cost a few dollars each and are visible from a goodly distance.  Also, get some clear lens glasses, especially if you are commuting near water sources.  There are a lot of airborne insects, flying debris, dust, etc that can get into your eyes. 

I'll be commuting through a rural area, so I'm concerned about lighting and visibility. I've never put lights on my bike before. Is it better to use headlights or some type of helmet lighting? Or does it matter? I want to be able to see and be seen.

I have both types of light. Bike mounted and helmet mounted.

You'll have to spend a lot of money to get a light that enables you to see things. Being seen is a much simpler matter.