It's the percentage of your total owned points. If you own 200 points and used 100 for a vacation, you have until the 50% deadline to bank 100 points.
Another example, You own 200 points. You used 75 points for your vacation so you have 125 left. If you are at the 50% banking deadline point, you'll still only be able to bank 50% of your total -- 100 points. 25 points will have to be used by the end of the Use Year.