If I understand correctly, you let WiiMC playing and it hide the controls bar… perfectly normal… just press a key on your Wiimote to turn it on again and point it at the screen, the controls/navigation bar should appear.
Now point it out of the screen, the controls/navigation bar should disappear, point it at the screen again and take a look at what happens… already understood how it works? 😀
Now let your Wiimote be “quiet” (don’t touch it, don’t point it a the screen) for 30 seconds and it should turn off, press a key to turn it on again. This is to save battery, if you don’t want it you can disable it in settings.