You could also use a hand towel to help keep them sturdy in the box.. I would use the cups, but only filled no more then halfway- that way it's easier to refresh their air. But bags are just fine and it does give them a little wiggle room in case of a bumpy ride- ask a local pet store for a few extra bags. Keep your glass thermometer handy to check the temp along the way- as cups/bags get cold/hot quickly and easily. If they are too warm (above 86*) then you can loosen the towel, if too cold (below 72*) then you can add another towel or wrap them up tighter.