How can you use a rate to compare the costs of 2 boxes of cereal that are different sizes

You'd have to use their weights and work out price/gram or you could alternately work out the volume (this is pretty hard because most cereals come in very awkward plastic containers so I recommend price/gram).

So just do this for both boxes:
Price / Mass (in grams)

The one with the greater value will be the less cost-effective method.