Brandon, I was training to prepare for the military and I was advised by many people not to run in boots on a regular basis. Yes, you should do it once in a while to get used to it because it is something you'll need to get used to, but if you do it as your usual choice of footwear, you may cause more harm than good.
I'm an advocate of barefoot running. For starters, it makes learning to run pose much easier because you don't have a big cushioned heal clipping the ground. Personally, I had rather flat feet and I overpronated quite a bit. Once I started running barefoot, my arch actually developed, and I don't overpronate nearly as much as I used to. I think my feet are much stronger now.
Before you start though, big warning, start light. When I first got my five fingers I was so pumped I went out and ran a 5K. I couldn't walk right for the rest of the week. So start off very light, lighter than you think is light. Good luck with your training!