I read it when I was young. A group of humans in one system are separated from a powerful human empire for several hundred years. The large empire accidentally finds them and slowly tries to conquer them over a period of books. The defenders are outnumbered and have small ships, but they have some sort of gate technology which allows them to move ships and torpedoes where the empire ships are not expecting them.
The Empire is described as overconfident. Eventually I remember they send a massive fleet and we follow its progress for some time.
I remember them as human, but they could be something else. Also, I believe, but am not sure, that the small group had some contact with an alien/religious species/order within their own system. They turned to them for advice/alliance as the books moved on.
Lastly, the gates were the huge point of much of the story. They allowed the weaker group to win time and again.