Has the vet checked the puppies out? I wonder if there is something wrong with the two small ones. Have you checked their palates for clefts? Are they eliminating well? Do they take the bottle well? How much do your puppies weigh so we can get an idea of what you are talking about with the difference in sizes. Be sure to weigh them all each day.
Take the blanket out of the box. You may also have to separate the mom from the puppies except every 2 hours to put them together for feeding and any time you can be there to watch them. That way she won't kill the pups. It is not uncommon for a mother dog to try to kill puppies, especially the smallest, or sickly ones. It is part of nature -- survival of the fitest. But -- you can intervene and SAVE the puppies by being vigilant and providing extra nurishment. The pups will also need heat. A puppy heating pad placed under one end of the whelping box works well. I used Rubbermade under bed boxes for the puppies and the heating pad managed to heat through the plastic just enough. You only want half of the whelping box heated. Thta way the pups can move to a cooler area if necessary. Heat lamps also work well. I used them at first but decided I liked the heating pads much better (I kept burning myself on the lamp
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If you or a family member is handy with wood, you might want to hurry and build a proper whelping box with a puppy rail to help protect them from being smothered:
How to Build a Whelping Box for Your Dog