Representing non-planar graphs with overlapping circles
The definitive article is a paper by Hlineny and Kratochvil from 2001. In it they show that the problem of recognizing a disk intersection graph (your question) is NP-hard, which suggests that it will be difficult to come up with a clean characterization. They also point out that $K_{3,3}$ cannot be represented as the intersection of disks, answering the other part of your question.