I have my orders of cupcakes for tomorrow.. (cupcakes with cream cheese frosting).. 
How should I store these cupcakes? Can i store the cupcakes in a cupcake box then cover the whole box with a saran wrap? 
and put it in a cool dry place? 

all that sounds ok

even more important some cream cheese icings need to stay under 40 degrees and can only be out of that temperature for a total of four hours before bacteria starts growing more abundantly

no it won't turn green and start eating it's way out of the packaging but it's no longer within the safe range

sure we've all eaten it and not died

but the four hour thing is proper food handling for some/most cream cheese food products

and i mispoke--the cream cheese itself can be out of temp for a total of four hours so factor in the time it rode around in the grocery cart and your car and how long it took to make the icing, apply to cakes etc.

not all cream cheese icings have to be kept chilled but cream cheese is considered a potentially hazardous food for this reason

I ice cupcakes with cream cheese all the time. I just put the cupcakes in a clamshell container (this is what I store all my cupcakes in) and put th whole thing in the frige.  This has never caused any of my cupcakes to become dry.