If it helps, I went to undergrad out-of-state, so like you, I had to take some of the pre-reqs online through other universities and had to talk through getting some courses waived. My school also did not offer a pre-vet major, but if you have a good advisor it all works out in the end. It was a huge stress, I'll admit. But I couldn't be happier where I'm at. And, to level things out, the interview process is the MMI style, so everyone is in the same boat there, regardless of where you went to school.
I guess what I'm saying is relax and take a deep breath (I know its hard...I was in your shoes last year).