How do we work our two rescued mares when they have seperation issues?

We rescued two mares. One is a small mustang and the other is a large quarter horse type. The large horse is the dominant mare. She is moody and nips at the smaller horse at times. But, when we halter and try to work them seperately, the smaller horse gets very antsy and upset if she is apart from the big horse. She tries to jump the fence and we are afraid she will hurt herself. She also gets spooked very easily. What is the best way to work them to build confidence and get them on the right track?