I'm currently writing my own exporter for Maya. The exporter is ment for characters and has support for bones and animation, but since I don't have too much experience with modeling, I don't know how models are usually built. For now my exporter only works with a single mesh. So my question is: Is it common to model with multiple meshes when building characters or do you start with a single mesh and just transform it?

You can (and usually do for games) combine all objects into a single mesh. You just need to make sure it supports multiple materials, a single mesh shouldn't be a problem.