Your crops, once harvested, will appear in your storage in the form of bags or boxes (depending on crop type).
If you hire someone to do your crops it will increase the sale price, this is marked with "Large."
Crops that you harvested yourself sell for less coins - these are labelled with the name of the product, not large.
It does not make a difference what size box the crop is, when used to make products in facilites. The order they are used in is regular box first, then large boxes, then if you have any from the gift page, those get used last.