I have an FBX character model with animation in it. Blender couldn't read it, so I've converted it using Autodesk FBX converter. Now when I import this model into Blender, it is scaled up, rotated in relation to its skeleton and whole mesh is oddly stretched.
Pay attention to the bottom left of your Blender screen on import (you may need to scroll down to see it).
There are options for both the mesh and the armature here, and you need to play around with the axis settings to match your workflow.
If you still have questions/issues with this, please comment to state what they are, and fix up the question to show more specific requests where you are having the issues. That way this post can serve as a decent reference to help others, who may run into similar issues.
If you answer your own question, please detail what you did to solve the problem.