Is there any reason why you couldn't have only one physical product and then link any size variations (i.e., carton) to a kit? The kit becomes the carton item and it subtracts multiples of the physical item when invoiced or ordered?
Another way to do this would be to bill in multiple units of measure. (Use box dimension table.)
But if you really needed to track them as separate quantities of each, then you could adjust stock more formally using Assembly Manager, but you would require Enterprise Edition or better to acquire that feature.