After importing a face into Facefx from Maya, the coordinates are off and my face is on its side. Is there any way to rotate the mesh in FaceFx? Or is it just something I have to adjust on the export from maya?
The best solution for you will just be to export a new FBX file. The "Autodesk Media & Entertainment" Preset FBX Export settings have the "Up Axis" as Y. Is that the setting you used? Is your content Y-up?
There are things you can do in the OGRE .SCENE file too, but those files are designed to be regenerated whenever you update your FBX file, so the best thing to do is fix it in the FBX file.