I'm making cupcakes to bring to school tomorrow and I plan on making cream cheese frosted cupcakes. I'm not sure if I should leave them out overnight covered or in the fridge. 

in the fridge -- in fact the cream cheese can only be out of the fridge for an accumulated total of 4 hours before the bacteria level is too high to eat -- it won't smell or taste bad but after four hours out of temp it would be dangerous to serve to the very young/old or anyone who is already sick or has a condition --

by accumulated total i mean the time it takes to get it off the shelf at the store and into your fridge, how long it takes to make the icing and decorate -- travel time to the school -- hold time -- add that all up and it needs to be under 4 hours or it's unsafe to serve

Well, that is not exactly accurate information. it is not total accumulated throughout the day..including in fridge and out of fridge. The actual FDA standard is: If at 2 hours the temperature of the food is above 41 degrees, then you can correct the problem by putting the cream cheese back in the fridge to reach the temp that it needs to be. If it is left out for 4 hours in one sitting, then it must be thrown away. Leaving it out for 5, 10 30, minutes at different intervals will does not make the bacteria grow. 

But K8memphis is correct in that it needs to be refrigerated overnight.

bacteria grows less in the refrigerator but it does not stop bacterial growth -- in fact some bacteria grow steadi!y even in the fridge for example listeria --

home refrigerators often do not have thermometers and are opened over and over by all the different members of the family so they are not holding foods at the proper temp anyway -- 

some of the pasty chefs i have worked with use the accumulated time schedule -- it's safe to do so -- the FDA gives their guidelines and each different local regulatory authority issues their own regulations to follow