Hello Raquisite,
Not a problem. This is what we are here for.
Inside of your skeletal mesh > Skeleton section you have your list of joints. You can reorient your joints there. There is no way, from here that you can reorient the mesh itself. So if you selected your root joint you reorient your skeleton there.
Upon import of an .fbx you have a menu for .fbx import options. There is a section that deals with translation and orientation.