I've heard some good things about this show, and have a couple on my DVR. Is this a show that I should watch in order? Am I gonna be lost if I start at a random episode?

Not really, they usually recap the previous episodes. It is good to see them in order, but not essential.

Considering they explain what certain things are, as well as the reasons why they do things, it's almost more helpful to start with later episodes anyway.

I've been getting them through Netflix, and there are 2 episodes per disc. What's the reasoning behind that?

I would say to beef up the box set so they could charge more, but last I saw, the boxset for season 1 anyway, was like 20 bucks.