Well, I am so sorry to hear of the little one that didn't make it but please do not let guilt dwell on you. It was just not meant to be and you and Ciara have four other beautiful babies to care for. Concentrate now on them and helping them to grow into beautiful Yorkshire Terriers.
Many people use some sort of colored bands/ribbons or such to distinguish between the puppies, but I agree that there is too much left hanging that could get caught up and possibly hurt a puppy. Definitely shorten them, make sure they are not to tight, and check them often. These little ones grow so quickly and you don't want the ribbons to get to tight and choke them.
Congratulations again, good luck, and keep the pictures coming!