When we took Pedro travelling with us, he used a box with newspapers. He really didn't like this! Even when he got use to it, it seemed like he would hold his poo until the last possible moment (i.e his little bum was portruding out!!!). I think dogs just dont find it natural to pee or poo in the same area. Also they prob instinctively like grass (mine will not pee or poo on hard floor unless he just can't hold it any longer!). You puppy will probably get it in time. maybe keep picking her up and moving her into the litter when she is mid pee or poo??