Your mom obviously was hungry ...nursing increases the appetite, and remember what goes in must come out
I would suggest buying an x-pen (which would confine the mom and pups together when you leave) with a bed large enough for the mom and the puppies. The x-pen will allow a place for their pee pads, food and water and still leaves plenty of room to play. This will also prevent mom from having "mistakes all over your house"
IMHO keeping pups in a box is not the best answer, moms need the ability to access the pups and the pups need access to her, a pee pad, food/water and a clean area to play.