Where did she come from a shelter, rescue or rehome? It really is hard to tell is it is confusion or that she is just not trained. If you have her tethered she wouldn't be able to run under the bed. Pebbles would always run under the bed too. So I started keeping her leash on her all the time, but then she got smart and would take the end of the leash with her if she decided to run away from me. Can you say too smart for her own good.
Only use positive reinforcement when she has accidents. Get a good enzyme carpet cleaner and just clean up the urine spots. If you don't clean the spots she will keep going in the same place.