We will be traveling east on the Glacier Express and are staying in Pontresina. Does the train stop in Samedan on the way to St Moritz? It does not look like it is a regular stop. From what I can tell we would need to get off there and get a regional train into Pontresina.
The Glacier Express train terminates at St Moritz, so yes you need to get off (everybody else on the train has to as well) and take a local train to Pontresina.
I don't know your dates or times and which trains you are planning on so I can't give a definite answer.
You can look it up yourself on the Swiss Federal Railways site: www.sbb.ch Just look up from <wherever you are starting> to Pontresina and it will tell you where to change. If you then click on the train ID for each individual train it will show all the stops.
That said, AFAIK all trains stop at Samedan.