I stopped moving and I can't cast spells. If you are out of Fatigue Points, then you are tired out and exhausted. You need to rest. If you are in the middle of a battle, then you are in trouble. Standing still gains you two Fatigue Points per second.
Runes get a number of charges based on the power level they are cast at.
Have a member of your team cast the Light magic skill's Reveal spell in often-travelled areas. Any Runes they find will be visible to your entire team. The Reveal spell also uncloaks anyone who is invisble. Cast the Light spell at them. They cancel each other out.