Yes you can use cool whip or whipped cream to thicken out pudding.
When making pudding you are supposed to use milk to add a creaming texture to the pudding and also make it more delicious and thick.
Some people use water when they do not have milk or when they are allergic to milk in the pudding.
Water is also okay when making pudding but milk is preferred because it makes the pudding thicker and creamier and adds a richer taste to the pudding.
But if you want to use whipped cream or cool whip to make the pudding with and to thicken the pudding the cool whip or whipped cream will work just fine at thickening the pudding.